1-163088404-T-C

Variant names:

• chr1-163088404-T-C
• rs2841959

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 0.478 in 151,204 control chromosomes in the GnomAD database, including 17,532 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 0.48 (17532 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.20
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.477 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: 0.478 AC: 72248 AN: 151088 Hom.: 17532 Cov.: 29

Gnomad AFR AF: 0.473

Gnomad AMI AF: 0.695

Gnomad AMR AF: 0.486

Gnomad ASJ AF: 0.553

Gnomad EAS AF: 0.469

Gnomad SAS AF: 0.472

Gnomad FIN AF: 0.480

Gnomad MID AF: 0.528

Gnomad NFE AF: 0.473

Gnomad OTH AF: 0.480

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

GnomAD4 genome AF: 0.478 AC: 72288 AN: 151204 Hom.: 17532 Cov.: 29 AF XY: 0.478 AC XY: 35280 AN XY: 73868

African (AFR) AF: 0.473 AC: 19483 AN: 41208

American (AMR) AF: 0.486 AC: 7377 AN: 15186

Ashkenazi Jewish (ASJ) AF: 0.553 AC: 1914 AN: 3460

East Asian (EAS) AF: 0.469 AC: 2411 AN: 5142

South Asian (SAS) AF: 0.471 AC: 2263 AN: 4800

European-Finnish (FIN) AF: 0.480 AC: 4971 AN: 10356

Middle Eastern (MID) AF: 0.524 AC: 154 AN: 294

European-Non Finnish (NFE) AF: 0.474 AC: 32087 AN: 67758

Other (OTH) AF: 0.477 AC: 1001 AN: 2098

Alfa AF: 0.477 Hom.: 51575

Bravo AF: 0.481

Asia WGS AF: 0.433 AC: 1501 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.88
DANN	Benign	0.71
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs2841959; hg19: chr1-163058194;