dbSNP rs16879308: ENSG00000300361:n.625-2721G>A (chr5-51940492-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 ENST00000771174.1(ENSG00000300361):n.625-2721G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0546 in 152,186 control chromosomes in the GnomAD database, including 232 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 ( 232 hom., cov: 33)

Consequence

ENSG00000300361
ENST00000771174.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.282

Publications

2 publications found

Variant links:

Genes affected

ENSG00000300361 (HGNC:):

ENSG00000300361 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=-0.9).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0703 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105378959	XR_948315.2 link	n.141-2721G>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000300361	ENST00000771174.1 link	n.625-2721G>A		intron_variant	Intron 2 of 5

Frequencies

GnomAD3 genomes

AF:

0.0547

AC:

8312

AN:

152068

Hom.:

232

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0564

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0395

Gnomad ASJ

AF:

0.0588

Gnomad EAS

AF:

0.000965

Gnomad SAS

AF:

0.0757

Gnomad FIN

AF:

0.0569

Gnomad MID

AF:

0.0380

Gnomad NFE

AF:

0.0598

Gnomad OTH

AF:

0.0574

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

GnomAD4 genome

AF:

0.0546

AC:

8316

AN:

152186

Hom.:

232

Cov.:

AF XY:

0.0547

AC XY:

4071

AN XY:

74404

show subpopulations

African (AFR)

AF:

0.0563

AC:

2338

AN:

41522

American (AMR)

AF:

0.0395

AC:

603

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.0588

AC:

204

AN:

3470

East Asian (EAS)

AF:

0.000967

AC:

AN:

5172

South Asian (SAS)

AF:

0.0768

AC:

370

AN:

4818

European-Finnish (FIN)

AF:

0.0569

AC:

603

AN:

10598

Middle Eastern (MID)

AF:

0.0374

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0597

AC:

4062

AN:

68006

Other (OTH)

AF:

0.0568

AC:

120

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

410

819

1229

1638

2048

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

188

282

376

470

<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:

0.0561

Hom.:

108

Bravo

AF:

0.0525

Asia WGS

AF:

0.0440

AC:

153

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

1.0

(source)

DANN

Benign

0.53

PhyloP100

0.28

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