1-162060117-A-T

Variant names:

• chr1-162060117-A-T
• rs4657139

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 0.477 in 152,124 control chromosomes in the GnomAD database, including 21,496 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 (21496 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.265
• Publications: 34 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.652 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: 0.477 AC: 72548 AN: 152006 Hom.: 21480 Cov.: 32

Gnomad AFR AF: 0.131

Gnomad AMI AF: 0.620

Gnomad AMR AF: 0.574

Gnomad ASJ AF: 0.608

Gnomad EAS AF: 0.282

Gnomad SAS AF: 0.333

Gnomad FIN AF: 0.635

Gnomad MID AF: 0.547

Gnomad NFE AF: 0.657

Gnomad OTH AF: 0.518

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

GnomAD4 genome AF: 0.477 AC: 72577 AN: 152124 Hom.: 21496 Cov.: 32 AF XY: 0.477 AC XY: 35448 AN XY: 74368

African (AFR) AF: 0.131 AC: 5437 AN: 41524

American (AMR) AF: 0.575 AC: 8794 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.608 AC: 2110 AN: 3472

East Asian (EAS) AF: 0.282 AC: 1458 AN: 5164

South Asian (SAS) AF: 0.336 AC: 1618 AN: 4816

European-Finnish (FIN) AF: 0.635 AC: 6712 AN: 10572

Middle Eastern (MID) AF: 0.551 AC: 162 AN: 294

European-Non Finnish (NFE) AF: 0.657 AC: 44635 AN: 67972

Other (OTH) AF: 0.516 AC: 1087 AN: 2108

Alfa AF: 0.566 Hom.: 3411

Bravo AF: 0.464

Asia WGS AF: 0.302 AC: 1052 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	3.3
DANN	Benign	0.60
PhyloP100		0.27

Splicing

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

Other links and lift over

dbSNP: rs4657139; hg19: chr1-162029907;