rs2778003

Variant names:

• chr1-157599404-G-A
• rs2778003

Your query was ambiguous. Multiple possible variants found:

• chr1-157599404-G-A
• chr1-157599404-G-C
• chr1-157599404-G-T

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 0.397 in 151,748 control chromosomes in the GnomAD database, including 12,743 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 0.40 (12743 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.974
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.707 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: 0.397 AC: 60194 AN: 151630 Hom.: 12726 Cov.: 30

Gnomad AFR AF: 0.283

Gnomad AMI AF: 0.430

Gnomad AMR AF: 0.465

Gnomad ASJ AF: 0.372

Gnomad EAS AF: 0.727

Gnomad SAS AF: 0.536

Gnomad FIN AF: 0.493

Gnomad MID AF: 0.357

Gnomad NFE AF: 0.402

Gnomad OTH AF: 0.394

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

GnomAD4 genome AF: 0.397 AC: 60251 AN: 151748 Hom.: 12743 Cov.: 30 AF XY: 0.407 AC XY: 30205 AN XY: 74142

African (AFR) AF: 0.283 AC: 11720 AN: 41372

American (AMR) AF: 0.465 AC: 7099 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.372 AC: 1288 AN: 3460

East Asian (EAS) AF: 0.727 AC: 3748 AN: 5158

South Asian (SAS) AF: 0.537 AC: 2571 AN: 4790

European-Finnish (FIN) AF: 0.493 AC: 5174 AN: 10490

Middle Eastern (MID) AF: 0.356 AC: 104 AN: 292

European-Non Finnish (NFE) AF: 0.402 AC: 27328 AN: 67908

Other (OTH) AF: 0.392 AC: 828 AN: 2110

Alfa AF: 0.395 Hom.: 36259

Bravo AF: 0.386

Asia WGS AF: 0.603 AC: 2097 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.3
DANN	Benign	0.84
PhyloP100		-0.97

Splicing

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

Other links and lift over

dbSNP: rs2778003; hg19: chr1-157569194;