1-162924526-G-T

Variant names:

• chr1-162924526-G-T
• rs1806753

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 0.595 in 152,038 control chromosomes in the GnomAD database, including 27,172 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 (27172 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.690
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.694 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.595 AC: 90416 AN: 151920 Hom.: 27131 Cov.: 33

Gnomad AFR AF: 0.647

Gnomad AMI AF: 0.595

Gnomad AMR AF: 0.589

Gnomad ASJ AF: 0.513

Gnomad EAS AF: 0.713

Gnomad SAS AF: 0.500

Gnomad FIN AF: 0.548

Gnomad MID AF: 0.566

Gnomad NFE AF: 0.574

Gnomad OTH AF: 0.609

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

GnomAD4 genome AF: 0.595 AC: 90508 AN: 152038 Hom.: 27172 Cov.: 33 AF XY: 0.593 AC XY: 44070 AN XY: 74306

African (AFR) AF: 0.648 AC: 26859 AN: 41476

American (AMR) AF: 0.588 AC: 8977 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.513 AC: 1777 AN: 3464

East Asian (EAS) AF: 0.713 AC: 3690 AN: 5172

South Asian (SAS) AF: 0.501 AC: 2412 AN: 4818

European-Finnish (FIN) AF: 0.548 AC: 5789 AN: 10558

Middle Eastern (MID) AF: 0.575 AC: 169 AN: 294

European-Non Finnish (NFE) AF: 0.574 AC: 39007 AN: 67966

Other (OTH) AF: 0.609 AC: 1285 AN: 2110

Alfa AF: 0.559 Hom.: 3756

Bravo AF: 0.606

Asia WGS AF: 0.620 AC: 2158 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.7
DANN	Benign	0.49
PhyloP100		0.69

Splicing

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

Other links and lift over

dbSNP: rs1806753; hg19: chr1-162894316;