rs164130

Variant names:

• chr1-162414313-G-A
• rs164130

Your query was ambiguous. Multiple possible variants found:

• chr1-162414313-G-A
• chr1-162414313-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 0.602 in 151,710 control chromosomes in the GnomAD database, including 27,718 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 0.60 (27718 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.539
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.648 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: 0.602 AC: 91309 AN: 151592 Hom.: 27686 Cov.: 30

Gnomad AFR AF: 0.655

Gnomad AMI AF: 0.590

Gnomad AMR AF: 0.574

Gnomad ASJ AF: 0.637

Gnomad EAS AF: 0.658

Gnomad SAS AF: 0.569

Gnomad FIN AF: 0.622

Gnomad MID AF: 0.650

Gnomad NFE AF: 0.570

Gnomad OTH AF: 0.611

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

GnomAD4 genome AF: 0.602 AC: 91397 AN: 151710 Hom.: 27718 Cov.: 30 AF XY: 0.605 AC XY: 44832 AN XY: 74110

African (AFR) AF: 0.655 AC: 27090 AN: 41386

American (AMR) AF: 0.574 AC: 8761 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.637 AC: 2210 AN: 3468

East Asian (EAS) AF: 0.659 AC: 3385 AN: 5140

South Asian (SAS) AF: 0.570 AC: 2725 AN: 4782

European-Finnish (FIN) AF: 0.622 AC: 6532 AN: 10494

Middle Eastern (MID) AF: 0.651 AC: 190 AN: 292

European-Non Finnish (NFE) AF: 0.570 AC: 38669 AN: 67880

Other (OTH) AF: 0.616 AC: 1299 AN: 2108

Alfa AF: 0.587 Hom.: 3435

Bravo AF: 0.604

Asia WGS AF: 0.620 AC: 2155 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.3
DANN	Benign	0.23
PhyloP100		-0.54

Splicing

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

Other links and lift over

dbSNP: rs164130; hg19: chr1-162384103;