chr7-137358578-A-T

Variant names:

• chr7-137358578-A-T
• rs161342

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 0.46 in 151,638 control chromosomes in the GnomAD database, including 16,049 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 0.46 (16049 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.00
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.49 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: 0.460 AC: 69686 AN: 151520 Hom.: 16038 Cov.: 32

Gnomad AFR AF: 0.496

Gnomad AMI AF: 0.463

Gnomad AMR AF: 0.453

Gnomad ASJ AF: 0.359

Gnomad EAS AF: 0.372

Gnomad SAS AF: 0.365

Gnomad FIN AF: 0.451

Gnomad MID AF: 0.436

Gnomad NFE AF: 0.459

Gnomad OTH AF: 0.460

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

GnomAD4 genome AF: 0.460 AC: 69717 AN: 151638 Hom.: 16049 Cov.: 32 AF XY: 0.454 AC XY: 33622 AN XY: 74094

African (AFR) AF: 0.495 AC: 20469 AN: 41310

American (AMR) AF: 0.453 AC: 6905 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.359 AC: 1243 AN: 3466

East Asian (EAS) AF: 0.373 AC: 1916 AN: 5142

South Asian (SAS) AF: 0.366 AC: 1764 AN: 4822

European-Finnish (FIN) AF: 0.451 AC: 4737 AN: 10512

Middle Eastern (MID) AF: 0.434 AC: 126 AN: 290

European-Non Finnish (NFE) AF: 0.459 AC: 31178 AN: 67854

Other (OTH) AF: 0.456 AC: 959 AN: 2102

Alfa AF: 0.464 Hom.: 2018

Bravo AF: 0.462

Asia WGS AF: 0.398 AC: 1384 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.0
DANN	Benign	0.50
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs161342; hg19: chr7-137043324;