rs11730410

Variant names:

• chr4-547806-C-T
• rs11730410

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 0.142 in 149,988 control chromosomes in the GnomAD database, including 1,558 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 (1558 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.305

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.21 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: 0.142 AC: 21237 AN: 149870 Hom.: 1551 Cov.: 30

Gnomad AFR AF: 0.163

Gnomad AMI AF: 0.156

Gnomad AMR AF: 0.112

Gnomad ASJ AF: 0.161

Gnomad EAS AF: 0.220

Gnomad SAS AF: 0.157

Gnomad FIN AF: 0.143

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.128

Gnomad OTH AF: 0.135

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

GnomAD4 genome AF: 0.142 AC: 21281 AN: 149988 Hom.: 1558 Cov.: 30 AF XY: 0.142 AC XY: 10378 AN XY: 73140

Gnomad4 AFR AF: 0.163

Gnomad4 AMR AF: 0.112

Gnomad4 ASJ AF: 0.161

Gnomad4 EAS AF: 0.220

Gnomad4 SAS AF: 0.157

Gnomad4 FIN AF: 0.143

Gnomad4 NFE AF: 0.128

Gnomad4 OTH AF: 0.136

Alfa AF: 0.133 Hom.: 356

Bravo AF: 0.138

Asia WGS AF: 0.173 AC: 599 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	6.7
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11730410; hg19: chr4-541595;