rs11730410

chr4-547806-C-T

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/exons	MANE	UniProt

Ensembl

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