rs7664706

chr4-81297603-C-T

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 0.315 in 151,982 control chromosomes in the GnomAD database, including 8,290 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 0.31 (8290 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.627

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.46 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: 0.315 AC: 47768 AN: 151864 Hom.: 8271 Cov.: 32

Gnomad AFR AF: 0.465

Gnomad AMI AF: 0.260

Gnomad AMR AF: 0.276

Gnomad ASJ AF: 0.253

Gnomad EAS AF: 0.180

Gnomad SAS AF: 0.215

Gnomad FIN AF: 0.234

Gnomad MID AF: 0.287

Gnomad NFE AF: 0.266

Gnomad OTH AF: 0.284

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

GnomAD4 genome AF: 0.315 AC: 47846 AN: 151982 Hom.: 8290 Cov.: 32 AF XY: 0.309 AC XY: 22927 AN XY: 74282

Gnomad4 AFR AF: 0.466

Gnomad4 AMR AF: 0.276

Gnomad4 ASJ AF: 0.253

Gnomad4 EAS AF: 0.181

Gnomad4 SAS AF: 0.216

Gnomad4 FIN AF: 0.234

Gnomad4 NFE AF: 0.266

Gnomad4 OTH AF: 0.283

Alfa AF: 0.318 Hom.: 1182

Bravo AF: 0.325

Asia WGS AF: 0.197 AC: 688 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	0.79
Dann	Benign	0.24

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7664706; hg19: chr4-82218757;