rs4844763

Variant names:

• chr1-209144590-C-T
• rs4844763

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 0.422 in 151,742 control chromosomes in the GnomAD database, including 14,062 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 0.42 (14062 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.948
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.469 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: 0.422 AC: 63973 AN: 151622 Hom.: 14052 Cov.: 31

Gnomad AFR AF: 0.345

Gnomad AMI AF: 0.378

Gnomad AMR AF: 0.438

Gnomad ASJ AF: 0.583

Gnomad EAS AF: 0.168

Gnomad SAS AF: 0.432

Gnomad FIN AF: 0.420

Gnomad MID AF: 0.592

Gnomad NFE AF: 0.474

Gnomad OTH AF: 0.487

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

GnomAD4 genome AF: 0.422 AC: 64007 AN: 151742 Hom.: 14062 Cov.: 31 AF XY: 0.419 AC XY: 31029 AN XY: 74126

African (AFR) AF: 0.345 AC: 14257 AN: 41334

American (AMR) AF: 0.437 AC: 6663 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.583 AC: 2021 AN: 3466

East Asian (EAS) AF: 0.168 AC: 860 AN: 5128

South Asian (SAS) AF: 0.434 AC: 2083 AN: 4802

European-Finnish (FIN) AF: 0.420 AC: 4414 AN: 10516

Middle Eastern (MID) AF: 0.589 AC: 172 AN: 292

European-Non Finnish (NFE) AF: 0.474 AC: 32177 AN: 67944

Other (OTH) AF: 0.481 AC: 1016 AN: 2114

Alfa AF: 0.436 Hom.: 2179

Bravo AF: 0.419

Asia WGS AF: 0.302 AC: 1050 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.51
DANN	Benign	0.46
PhyloP100		-0.95

Splicing

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

Other links and lift over

dbSNP: rs4844763; hg19: chr1-209317935; COSMIC: COSV69221914;