7-116522675-G-A

Variant names:

• chr7-116522675-G-A
• rs4236601

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 0.274 in 152,128 control chromosomes in the GnomAD database, including 6,358 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 0.27 (6358 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.353
• Publications: 86 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.366 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.274 AC: 41718 AN: 152010 Hom.: 6356 Cov.: 32

Gnomad AFR AF: 0.371

Gnomad AMI AF: 0.378

Gnomad AMR AF: 0.223

Gnomad ASJ AF: 0.345

Gnomad EAS AF: 0.0114

Gnomad SAS AF: 0.200

Gnomad FIN AF: 0.137

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.268

Gnomad OTH AF: 0.294

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

GnomAD4 genome AF: 0.274 AC: 41744 AN: 152128 Hom.: 6358 Cov.: 32 AF XY: 0.264 AC XY: 19658 AN XY: 74380

African (AFR) AF: 0.371 AC: 15378 AN: 41464

American (AMR) AF: 0.223 AC: 3405 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.345 AC: 1198 AN: 3472

East Asian (EAS) AF: 0.0114 AC: 59 AN: 5182

South Asian (SAS) AF: 0.200 AC: 965 AN: 4826

European-Finnish (FIN) AF: 0.137 AC: 1455 AN: 10592

Middle Eastern (MID) AF: 0.299 AC: 88 AN: 294

European-Non Finnish (NFE) AF: 0.268 AC: 18237 AN: 67988

Other (OTH) AF: 0.291 AC: 614 AN: 2112

Alfa AF: 0.273 Hom.: 19328

Bravo AF: 0.287

Asia WGS AF: 0.0990 AC: 347 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	3.2
DANN	Benign	0.30
PhyloP100		0.35

Splicing

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

Other links and lift over

dbSNP: rs4236601; hg19: chr7-116162729;