chr1-186992194-T-G

Variant names:

• chr1-186992194-T-G
• rs761516

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 0.723 in 152,088 control chromosomes in the GnomAD database, including 41,148 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 0.72 (41148 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0320
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.853 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: 0.723 AC: 109833 AN: 151970 Hom.: 41119 Cov.: 32

Gnomad AFR AF: 0.514

Gnomad AMI AF: 0.860

Gnomad AMR AF: 0.722

Gnomad ASJ AF: 0.829

Gnomad EAS AF: 0.874

Gnomad SAS AF: 0.866

Gnomad FIN AF: 0.844

Gnomad MID AF: 0.687

Gnomad NFE AF: 0.802

Gnomad OTH AF: 0.708

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

GnomAD4 genome AF: 0.723 AC: 109909 AN: 152088 Hom.: 41148 Cov.: 32 AF XY: 0.729 AC XY: 54230 AN XY: 74360

African (AFR) AF: 0.514 AC: 21329 AN: 41460

American (AMR) AF: 0.722 AC: 11033 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.829 AC: 2879 AN: 3472

East Asian (EAS) AF: 0.874 AC: 4521 AN: 5170

South Asian (SAS) AF: 0.866 AC: 4182 AN: 4828

European-Finnish (FIN) AF: 0.844 AC: 8941 AN: 10594

Middle Eastern (MID) AF: 0.684 AC: 201 AN: 294

European-Non Finnish (NFE) AF: 0.802 AC: 54538 AN: 67970

Other (OTH) AF: 0.711 AC: 1501 AN: 2110

Alfa AF: 0.669 Hom.: 4344

Bravo AF: 0.700

Asia WGS AF: 0.838 AC: 2913 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.9
DANN	Benign	0.78
PhyloP100		-0.032

Splicing

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

Other links and lift over

dbSNP: rs761516; hg19: chr1-186961326;