rs11728679

Variant names:

• chr4-188166932-C-T
• rs11728679

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 0.136 in 151,974 control chromosomes in the GnomAD database, including 1,460 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 0.14 (1460 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.104

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.142 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: 0.136 AC: 20652 AN: 151858 Hom.: 1461 Cov.: 31

Gnomad AFR AF: 0.144

Gnomad AMI AF: 0.180

Gnomad AMR AF: 0.121

Gnomad ASJ AF: 0.116

Gnomad EAS AF: 0.0739

Gnomad SAS AF: 0.0769

Gnomad FIN AF: 0.130

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.144

Gnomad OTH AF: 0.147

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

GnomAD4 genome AF: 0.136 AC: 20651 AN: 151974 Hom.: 1460 Cov.: 31 AF XY: 0.132 AC XY: 9828 AN XY: 74260

Gnomad4 AFR AF: 0.143

Gnomad4 AMR AF: 0.121

Gnomad4 ASJ AF: 0.116

Gnomad4 EAS AF: 0.0743

Gnomad4 SAS AF: 0.0770

Gnomad4 FIN AF: 0.130

Gnomad4 NFE AF: 0.144

Gnomad4 OTH AF: 0.146

Alfa AF: 0.137 Hom.: 163

Bravo AF: 0.136

Asia WGS AF: 0.0790 AC: 274 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.4
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11728679; hg19: chr4-189088086;