rs499163

Variant names:

• chr1-43110067-G-A
• rs499163

Your query was ambiguous. Multiple possible variants found:

• chr1-43110067-G-A
• chr1-43110067-G-C

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 0.43 in 151,994 control chromosomes in the GnomAD database, including 17,075 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 0.43 (17075 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0640
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.578 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: 0.430 AC: 65301 AN: 151876 Hom.: 17069 Cov.: 32

Gnomad AFR AF: 0.120

Gnomad AMI AF: 0.719

Gnomad AMR AF: 0.457

Gnomad ASJ AF: 0.532

Gnomad EAS AF: 0.453

Gnomad SAS AF: 0.485

Gnomad FIN AF: 0.517

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.582

Gnomad OTH AF: 0.466

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

GnomAD4 genome AF: 0.430 AC: 65304 AN: 151994 Hom.: 17075 Cov.: 32 AF XY: 0.428 AC XY: 31800 AN XY: 74264

African (AFR) AF: 0.120 AC: 4969 AN: 41462

American (AMR) AF: 0.456 AC: 6964 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.532 AC: 1846 AN: 3472

East Asian (EAS) AF: 0.453 AC: 2345 AN: 5180

South Asian (SAS) AF: 0.486 AC: 2337 AN: 4812

European-Finnish (FIN) AF: 0.517 AC: 5425 AN: 10502

Middle Eastern (MID) AF: 0.575 AC: 168 AN: 292

European-Non Finnish (NFE) AF: 0.582 AC: 39602 AN: 67988

Other (OTH) AF: 0.470 AC: 992 AN: 2110

Alfa AF: 0.368 Hom.: 1267

Bravo AF: 0.412

Asia WGS AF: 0.455 AC: 1583 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	5.9
DANN	Benign	0.53
PhyloP100		0.064

Splicing

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

Other links and lift over

dbSNP: rs499163; hg19: chr1-43575738; COSMIC: COSV59941620;