rs7685923

chr4-11080525-T-A

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/exons	MANE	UniProt

Ensembl

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