rs7691216

chr4-85208463-T-G

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;