rs7691216

Variant names:

• chr4-85208463-T-G
• rs7691216

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.482

Gnomad4 AMR AF: 0.234

Gnomad4 ASJ AF: 0.185

Gnomad4 EAS AF: 0.0651

Gnomad4 SAS AF: 0.257

Gnomad4 FIN AF: 0.187

Gnomad4 NFE AF: 0.191

Gnomad4 OTH AF: 0.263

Alfa AF: 0.244 Hom.: 748

Bravo AF: 0.285

Asia WGS AF: 0.183 AC: 634 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7691216; hg19: chr4-86129616;