rs7685923

Variant names:

• chr4-11080525-T-A
• rs7685923

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 0.184 in 150,630 control chromosomes in the GnomAD database, including 2,985 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 0.18 (2985 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.555

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.289 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: 0.184 AC: 27675 AN: 150544 Hom.: 2962 Cov.: 30

Gnomad AFR AF: 0.293

Gnomad AMI AF: 0.235

Gnomad AMR AF: 0.180

Gnomad ASJ AF: 0.121

Gnomad EAS AF: 0.147

Gnomad SAS AF: 0.184

Gnomad FIN AF: 0.163

Gnomad MID AF: 0.154

Gnomad NFE AF: 0.127

Gnomad OTH AF: 0.189

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

GnomAD4 genome AF: 0.184 AC: 27746 AN: 150630 Hom.: 2985 Cov.: 30 AF XY: 0.186 AC XY: 13676 AN XY: 73470

Gnomad4 AFR AF: 0.293

Gnomad4 AMR AF: 0.181

Gnomad4 ASJ AF: 0.121

Gnomad4 EAS AF: 0.147

Gnomad4 SAS AF: 0.184

Gnomad4 FIN AF: 0.163

Gnomad4 NFE AF: 0.127

Gnomad4 OTH AF: 0.193

Alfa AF: 0.165 Hom.: 277

Bravo AF: 0.192

Asia WGS AF: 0.194 AC: 675 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	8.8
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7685923; hg19: chr4-11082149;