rs7664706

Variant names:

• chr4-81297603-C-T
• rs7664706

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 0.315 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
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.466 AC: 19290 AN: 41426

American (AMR) AF: 0.276 AC: 4217 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.253 AC: 878 AN: 3468

East Asian (EAS) AF: 0.181 AC: 934 AN: 5164

South Asian (SAS) AF: 0.216 AC: 1041 AN: 4816

European-Finnish (FIN) AF: 0.234 AC: 2474 AN: 10558

Middle Eastern (MID) AF: 0.274 AC: 80 AN: 292

European-Non Finnish (NFE) AF: 0.266 AC: 18097 AN: 67968

Other (OTH) AF: 0.283 AC: 598 AN: 2112

Alfa AF: 0.368 Hom.: 2712

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
PhyloP100		-0.63

Splicing

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

Other links and lift over

dbSNP: rs7664706; hg19: chr4-82218757;