Genetic Variant NM_001728.4:c.*524G>A (chr19-583268-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001728.4(BSG):c.*524G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.055 in 152,474 control chromosomes in the GnomAD database, including 372 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.055 ( 372 hom., cov: 33)

Exomes 𝑓: 0.056 ( 0 hom. )

Consequence

BSG
NM_001728.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.24

Publications

8 publications found

Variant links:

Genes affected

BSG (HGNC:1116): (basigin (Ok blood group)) The protein encoded by this gene, basigin, is a plasma membrane protein that is important in spermatogenesis, embryo implantation, neural network formation, and tumor progression. Basigin is also a member of the immunoglobulin superfamily, ubiquitously expressed in various tissues. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, May 2020]

BSG links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.82).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.128 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001728.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
BSG	NM_001728.4	MANE Select	c.*524G>A	3_prime_UTR	Exon 9 of 9	NP_001719.2
BSG	NM_001322243.2		c.*520G>A	3_prime_UTR	Exon 8 of 8	NP_001309172.1
BSG	NM_198589.3		c.*524G>A	3_prime_UTR	Exon 8 of 8	NP_940991.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
BSG	ENST00000333511.9	TSL:1 MANE Select	c.*524G>A	3_prime_UTR	Exon 9 of 9	ENSP00000333769.3
BSG	ENST00000353555.9	TSL:1	c.*524G>A	3_prime_UTR	Exon 8 of 8	ENSP00000343809.4
BSG	ENST00000346916.9	TSL:1	c.*524G>A	3_prime_UTR	Exon 7 of 7	ENSP00000344707.4

Frequencies

GnomAD3 genomes

AF:

0.0551

AC:

8382

AN:

152178

Hom.:

371

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0142

Gnomad AMI

AF:

0.00901

Gnomad AMR

AF:

0.133

Gnomad ASJ

AF:

0.0357

Gnomad EAS

AF:

0.0169

Gnomad SAS

AF:

0.102

Gnomad FIN

AF:

0.0589

Gnomad MID

AF:

0.0443

Gnomad NFE

AF:

0.0628

Gnomad OTH

AF:

0.0626

GnomAD4 exome

AF:

0.0562

AC:

AN:

178

Hom.:

Cov.:

AF XY:

0.0328

AC XY:

AN XY:

122

show subpopulations

African (AFR)

AF:

0.250

AC:

AN:

American (AMR)

AF:

0.500

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AF:

0.167

AC:

AN:

European-Finnish (FIN)

AF:

0.00

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.0467

AC:

AN:

150

Other (OTH)

AF:

0.00

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.430

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0550

AC:

8379

AN:

152296

Hom.:

372

Cov.:

AF XY:

0.0581

AC XY:

4327

AN XY:

74462

show subpopulations

African (AFR)

AF:

0.0142

AC:

590

AN:

41570

American (AMR)

AF:

0.133

AC:

2037

AN:

15306

Ashkenazi Jewish (ASJ)

AF:

0.0357

AC:

124

AN:

3470

East Asian (EAS)

AF:

0.0168

AC:

AN:

5190

South Asian (SAS)

AF:

0.102

AC:

491

AN:

4830

European-Finnish (FIN)

AF:

0.0589

AC:

625

AN:

10614

Middle Eastern (MID)

AF:

0.0374

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0628

AC:

4275

AN:

68020

Other (OTH)

AF:

0.0620

AC:

131

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

402

804

1206

1608

2010

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

104

208

312

416

520

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0604

Hom.:

591

Bravo

AF:

0.0576

Asia WGS

AF:

0.0540

AC:

186

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

3.1

(source)

DANN

Benign

0.62

PhyloP100

-1.2

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over