chr3-1960118-G-T

Variant names:

• chr3-1960118-G-T
• rs1488745

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 0.561 in 151,974 control chromosomes in the GnomAD database, including 26,414 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 0.56 (26414 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.286
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.832 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: 0.561 AC: 85118 AN: 151856 Hom.: 26358 Cov.: 32

Gnomad AFR AF: 0.839

Gnomad AMI AF: 0.317

Gnomad AMR AF: 0.586

Gnomad ASJ AF: 0.447

Gnomad EAS AF: 0.314

Gnomad SAS AF: 0.496

Gnomad FIN AF: 0.484

Gnomad MID AF: 0.472

Gnomad NFE AF: 0.430

Gnomad OTH AF: 0.541

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

GnomAD4 genome AF: 0.561 AC: 85236 AN: 151974 Hom.: 26414 Cov.: 32 AF XY: 0.560 AC XY: 41603 AN XY: 74250

African (AFR) AF: 0.840 AC: 34823 AN: 41476

American (AMR) AF: 0.587 AC: 8958 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.447 AC: 1551 AN: 3472

East Asian (EAS) AF: 0.314 AC: 1619 AN: 5158

South Asian (SAS) AF: 0.495 AC: 2381 AN: 4810

European-Finnish (FIN) AF: 0.484 AC: 5089 AN: 10520

Middle Eastern (MID) AF: 0.473 AC: 139 AN: 294

European-Non Finnish (NFE) AF: 0.430 AC: 29248 AN: 67952

Other (OTH) AF: 0.540 AC: 1139 AN: 2108

Alfa AF: 0.468 Hom.: 28622

Bravo AF: 0.577

Asia WGS AF: 0.467 AC: 1628 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.5
DANN	Benign	0.40
PhyloP100		-0.29

Splicing

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

Other links and lift over

dbSNP: rs1488745; hg19: chr3-2001802;