rs381387

Variant names:

• chr2-79034122-T-C
• rs381387

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.843 in 152,172 control chromosomes in the GnomAD database, including 54,154 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 0.84 (54154 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.693
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.884 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.843 AC: 128208 AN: 152054 Hom.: 54099 Cov.: 32

Gnomad AFR AF: 0.854

Gnomad AMI AF: 0.900

Gnomad AMR AF: 0.849

Gnomad ASJ AF: 0.782

Gnomad EAS AF: 0.906

Gnomad SAS AF: 0.855

Gnomad FIN AF: 0.896

Gnomad MID AF: 0.796

Gnomad NFE AF: 0.825

Gnomad OTH AF: 0.820

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

GnomAD4 genome AF: 0.843 AC: 128321 AN: 152172 Hom.: 54154 Cov.: 32 AF XY: 0.845 AC XY: 62877 AN XY: 74390

African (AFR) AF: 0.854 AC: 35465 AN: 41506

American (AMR) AF: 0.849 AC: 12972 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.782 AC: 2712 AN: 3470

East Asian (EAS) AF: 0.906 AC: 4678 AN: 5166

South Asian (SAS) AF: 0.856 AC: 4127 AN: 4824

European-Finnish (FIN) AF: 0.896 AC: 9496 AN: 10602

Middle Eastern (MID) AF: 0.791 AC: 231 AN: 292

European-Non Finnish (NFE) AF: 0.825 AC: 56084 AN: 68018

Other (OTH) AF: 0.822 AC: 1737 AN: 2112

Alfa AF: 0.841 Hom.: 6985

Bravo AF: 0.843

Asia WGS AF: 0.893 AC: 3106 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.9
DANN	Benign	0.58
PhyloP100		-0.69

Splicing

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

Other links and lift over

dbSNP: rs381387; hg19: chr2-79261248;