Genetic Variant LOC105377158:n.405+1937G>A (chr3-72300712-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The XR_001740748.3(LOC105377158):n.405+1937G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.295 in 152,108 control chromosomes in the GnomAD database, including 6,848 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 0.29 ( 6848 hom., cov: 32)

Consequence

LOC105377158
XR_001740748.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.06

Publications

2 publications found

Variant links:

Genes affected

LOC105377158 (HGNC:):

LOC105377158 links:

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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=-0.92).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.393 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
LOC105377158	XR_001740748.3 link	n.405+1937G>A	intron_variant	Intron 3 of 5
LOC105377158	XR_001740749.3 link	n.321+1937G>A	intron_variant	Intron 3 of 5
LOC105377158	XR_001740750.3 link	n.405+1937G>A	intron_variant	Intron 3 of 4
LOC105377158	XR_940959.2 link	n.405+1937G>A	intron_variant	Intron 3 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes

AF:

0.295

AC:

44785

AN:

151990

Hom.:

6851

Cov.:

show subpopulations

Gnomad AFR

AF:

0.368

Gnomad AMI

AF:

0.345

Gnomad AMR

AF:

0.307

Gnomad ASJ

AF:

0.264

Gnomad EAS

AF:

0.408

Gnomad SAS

AF:

0.297

Gnomad FIN

AF:

0.207

Gnomad MID

AF:

0.282

Gnomad NFE

AF:

0.253

Gnomad OTH

AF:

0.286

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.295

AC:

44804

AN:

152108

Hom.:

6848

Cov.:

AF XY:

0.293

AC XY:

21763

AN XY:

74352

show subpopulations

African (AFR)

AF:

0.368

AC:

15236

AN:

41446

American (AMR)

AF:

0.307

AC:

4688

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.264

AC:

917

AN:

3470

East Asian (EAS)

AF:

0.408

AC:

2107

AN:

5166

South Asian (SAS)

AF:

0.296

AC:

1426

AN:

4820

European-Finnish (FIN)

AF:

0.207

AC:

2189

AN:

10594

Middle Eastern (MID)

AF:

0.282

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.253

AC:

17239

AN:

68016

Other (OTH)

AF:

0.286

AC:

604

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1627

3254

4881

6508

8135

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

454

908

1362

1816

2270

<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:

0.264

Hom.:

4717

Bravo

AF:

0.307

Asia WGS

AF:

0.338

AC:

1177

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

2.0

(source)

DANN

Benign

0.61

PhyloP100

-1.1

Splicing

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over