rs619879

Variant names:

• chr1-103944526-G-A
• rs619879

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 0.295 in 151,772 control chromosomes in the GnomAD database, including 6,970 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 0.30 (6970 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.517
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.348 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: 0.295 AC: 44788 AN: 151654 Hom.: 6964 Cov.: 31

Gnomad AFR AF: 0.208

Gnomad AMI AF: 0.333

Gnomad AMR AF: 0.355

Gnomad ASJ AF: 0.262

Gnomad EAS AF: 0.210

Gnomad SAS AF: 0.357

Gnomad FIN AF: 0.264

Gnomad MID AF: 0.394

Gnomad NFE AF: 0.342

Gnomad OTH AF: 0.319

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

GnomAD4 genome AF: 0.295 AC: 44812 AN: 151772 Hom.: 6970 Cov.: 31 AF XY: 0.295 AC XY: 21844 AN XY: 74172

African (AFR) AF: 0.208 AC: 8611 AN: 41448

American (AMR) AF: 0.356 AC: 5407 AN: 15198

Ashkenazi Jewish (ASJ) AF: 0.262 AC: 908 AN: 3466

East Asian (EAS) AF: 0.210 AC: 1077 AN: 5136

South Asian (SAS) AF: 0.358 AC: 1725 AN: 4824

European-Finnish (FIN) AF: 0.264 AC: 2786 AN: 10558

Middle Eastern (MID) AF: 0.393 AC: 114 AN: 290

European-Non Finnish (NFE) AF: 0.342 AC: 23213 AN: 67834

Other (OTH) AF: 0.317 AC: 667 AN: 2106

Alfa AF: 0.321 Hom.: 2113

Bravo AF: 0.298

Asia WGS AF: 0.321 AC: 1115 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.68
DANN	Benign	0.15
PhyloP100		-0.52

Splicing

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

Other links and lift over

dbSNP: rs619879; hg19: chr1-104487148;