7-136657741-A-T

Variant names:

• chr7-136657741-A-T
• rs17168743

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 0.211 in 151,898 control chromosomes in the GnomAD database, including 4,552 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 0.21 (4552 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.245
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.401 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: 0.210 AC: 31928 AN: 151778 Hom.: 4538 Cov.: 32

Gnomad AFR AF: 0.406

Gnomad AMI AF: 0.183

Gnomad AMR AF: 0.122

Gnomad ASJ AF: 0.152

Gnomad EAS AF: 0.00251

Gnomad SAS AF: 0.118

Gnomad FIN AF: 0.127

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.150

Gnomad OTH AF: 0.201

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

GnomAD4 genome AF: 0.211 AC: 31988 AN: 151898 Hom.: 4552 Cov.: 32 AF XY: 0.204 AC XY: 15181 AN XY: 74236

African (AFR) AF: 0.407 AC: 16841 AN: 41420

American (AMR) AF: 0.122 AC: 1858 AN: 15216

Ashkenazi Jewish (ASJ) AF: 0.152 AC: 527 AN: 3466

East Asian (EAS) AF: 0.00252 AC: 13 AN: 5160

South Asian (SAS) AF: 0.119 AC: 572 AN: 4820

European-Finnish (FIN) AF: 0.127 AC: 1340 AN: 10584

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.150 AC: 10208 AN: 67918

Other (OTH) AF: 0.199 AC: 419 AN: 2108

Alfa AF: 0.0892 Hom.: 143

Bravo AF: 0.221

Asia WGS AF: 0.0680 AC: 236 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.6
DANN	Benign	0.31
PhyloP100		-0.24

Splicing

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

Other links and lift over

dbSNP: rs17168743; hg19: chr7-136342489;