rs7694207

Variant names:

• chr4-96959258-C-T
• rs7694207

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 0.281 in 152,052 control chromosomes in the GnomAD database, including 6,872 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 0.28 (6872 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.17
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.421 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: 0.281 AC: 42700 AN: 151934 Hom.: 6851 Cov.: 33

Gnomad AFR AF: 0.426

Gnomad AMI AF: 0.337

Gnomad AMR AF: 0.218

Gnomad ASJ AF: 0.311

Gnomad EAS AF: 0.124

Gnomad SAS AF: 0.354

Gnomad FIN AF: 0.128

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.233

Gnomad OTH AF: 0.312

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

GnomAD4 genome AF: 0.281 AC: 42748 AN: 152052 Hom.: 6872 Cov.: 33 AF XY: 0.279 AC XY: 20719 AN XY: 74328

African (AFR) AF: 0.427 AC: 17697 AN: 41488

American (AMR) AF: 0.218 AC: 3327 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.311 AC: 1081 AN: 3472

East Asian (EAS) AF: 0.123 AC: 637 AN: 5172

South Asian (SAS) AF: 0.354 AC: 1710 AN: 4828

European-Finnish (FIN) AF: 0.128 AC: 1358 AN: 10578

Middle Eastern (MID) AF: 0.405 AC: 119 AN: 294

European-Non Finnish (NFE) AF: 0.233 AC: 15858 AN: 67942

Other (OTH) AF: 0.310 AC: 654 AN: 2112

Alfa AF: 0.258 Hom.: 15987

Bravo AF: 0.293

Asia WGS AF: 0.237 AC: 824 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.93
DANN	Benign	0.66
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs7694207; hg19: chr4-97880409;