rs7691216

Variant names:

• chr4-85208463-T-G
• rs7691216

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 151,948 control chromosomes in the GnomAD database, including 7,013 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 (7013 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.23
• 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 = 0.477 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: 0.274 AC: 41599 AN: 151830 Hom.: 7005 Cov.: 32

Gnomad AFR AF: 0.483

Gnomad AMI AF: 0.338

Gnomad AMR AF: 0.234

Gnomad ASJ AF: 0.185

Gnomad EAS AF: 0.0650

Gnomad SAS AF: 0.257

Gnomad FIN AF: 0.187

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.191

Gnomad OTH AF: 0.266

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

GnomAD4 genome AF: 0.274 AC: 41640 AN: 151948 Hom.: 7013 Cov.: 32 AF XY: 0.271 AC XY: 20146 AN XY: 74296

African (AFR) AF: 0.482 AC: 19969 AN: 41396

American (AMR) AF: 0.234 AC: 3562 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.185 AC: 643 AN: 3470

East Asian (EAS) AF: 0.0651 AC: 338 AN: 5190

South Asian (SAS) AF: 0.257 AC: 1237 AN: 4818

European-Finnish (FIN) AF: 0.187 AC: 1967 AN: 10528

Middle Eastern (MID) AF: 0.279 AC: 82 AN: 294

European-Non Finnish (NFE) AF: 0.191 AC: 12980 AN: 67976

Other (OTH) AF: 0.263 AC: 555 AN: 2114

Alfa AF: 0.317 Hom.: 3453

Bravo AF: 0.285

Asia WGS AF: 0.183 AC: 634 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.33
DANN	Benign	0.73
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs7691216; hg19: chr4-86129616;