chr1-164987729-T-G

Variant names:

• chr1-164987729-T-G
• rs4656422

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 0.655 in 151,834 control chromosomes in the GnomAD database, including 34,960 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 0.66 (34960 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.468
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.918 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: 0.656 AC: 99466 AN: 151716 Hom.: 34952 Cov.: 30

Gnomad AFR AF: 0.388

Gnomad AMI AF: 0.676

Gnomad AMR AF: 0.759

Gnomad ASJ AF: 0.644

Gnomad EAS AF: 0.940

Gnomad SAS AF: 0.802

Gnomad FIN AF: 0.760

Gnomad MID AF: 0.737

Gnomad NFE AF: 0.746

Gnomad OTH AF: 0.679

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

GnomAD4 genome AF: 0.655 AC: 99505 AN: 151834 Hom.: 34960 Cov.: 30 AF XY: 0.662 AC XY: 49134 AN XY: 74204

African (AFR) AF: 0.387 AC: 16028 AN: 41390

American (AMR) AF: 0.759 AC: 11568 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.644 AC: 2237 AN: 3472

East Asian (EAS) AF: 0.940 AC: 4830 AN: 5140

South Asian (SAS) AF: 0.802 AC: 3853 AN: 4806

European-Finnish (FIN) AF: 0.760 AC: 8006 AN: 10538

Middle Eastern (MID) AF: 0.741 AC: 218 AN: 294

European-Non Finnish (NFE) AF: 0.746 AC: 50712 AN: 67946

Other (OTH) AF: 0.683 AC: 1439 AN: 2106

Alfa AF: 0.705 Hom.: 17758

Bravo AF: 0.644

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.6
DANN	Benign	0.83
PhyloP100		0.47

Splicing

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

Other links and lift over

dbSNP: rs4656422; hg19: chr1-164956966;