rs4387163

Variant names:

• chr1-165026476-G-A
• rs4387163

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 0.449 in 152,022 control chromosomes in the GnomAD database, including 19,174 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 0.45 (19174 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.968
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.611 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.450 AC: 68296 AN: 151904 Hom.: 19181 Cov.: 32

Gnomad AFR AF: 0.110

Gnomad AMI AF: 0.679

Gnomad AMR AF: 0.407

Gnomad ASJ AF: 0.524

Gnomad EAS AF: 0.513

Gnomad SAS AF: 0.466

Gnomad FIN AF: 0.681

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.616

Gnomad OTH AF: 0.480

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

GnomAD4 genome AF: 0.449 AC: 68276 AN: 152022 Hom.: 19174 Cov.: 32 AF XY: 0.450 AC XY: 33462 AN XY: 74300

African (AFR) AF: 0.110 AC: 4554 AN: 41510

American (AMR) AF: 0.407 AC: 6199 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.524 AC: 1819 AN: 3472

East Asian (EAS) AF: 0.514 AC: 2650 AN: 5158

South Asian (SAS) AF: 0.466 AC: 2247 AN: 4818

European-Finnish (FIN) AF: 0.681 AC: 7204 AN: 10572

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

European-Non Finnish (NFE) AF: 0.616 AC: 41827 AN: 67934

Other (OTH) AF: 0.476 AC: 1004 AN: 2108

Alfa AF: 0.557 Hom.: 76476

Bravo AF: 0.414

Asia WGS AF: 0.439 AC: 1526 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.47
DANN	Benign	0.77
PhyloP100		-0.97

Splicing

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

Other links and lift over

dbSNP: rs4387163; hg19: chr1-164995713;