7-128911686-T-C

Variant names:

• chr7-128911686-T-C
• rs1495461

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 0.312 in 151,992 control chromosomes in the GnomAD database, including 7,590 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 0.31 (7590 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0150
• Publications: 14 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.358 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: 0.312 AC: 47423 AN: 151874 Hom.: 7578 Cov.: 32

Gnomad AFR AF: 0.363

Gnomad AMI AF: 0.398

Gnomad AMR AF: 0.287

Gnomad ASJ AF: 0.322

Gnomad EAS AF: 0.150

Gnomad SAS AF: 0.283

Gnomad FIN AF: 0.317

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.298

Gnomad OTH AF: 0.326

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

GnomAD4 genome AF: 0.312 AC: 47465 AN: 151992 Hom.: 7590 Cov.: 32 AF XY: 0.311 AC XY: 23067 AN XY: 74280

African (AFR) AF: 0.363 AC: 15018 AN: 41428

American (AMR) AF: 0.288 AC: 4397 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.322 AC: 1118 AN: 3470

East Asian (EAS) AF: 0.151 AC: 780 AN: 5180

South Asian (SAS) AF: 0.282 AC: 1357 AN: 4806

European-Finnish (FIN) AF: 0.317 AC: 3355 AN: 10572

Middle Eastern (MID) AF: 0.364 AC: 107 AN: 294

European-Non Finnish (NFE) AF: 0.298 AC: 20281 AN: 67950

Other (OTH) AF: 0.328 AC: 691 AN: 2106

Alfa AF: 0.299 Hom.: 20546

Bravo AF: 0.312

Asia WGS AF: 0.239 AC: 834 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	7.6
DANN	Benign	0.51
PhyloP100		0.015

Splicing

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

Other links and lift over

dbSNP: rs1495461; hg19: chr7-128551740;