rs11241713

chr5-123783871-C-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 0.114 in 151,354 control chromosomes in the GnomAD database, including 1,612 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 0.11 (1612 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0250

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.521 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: 0.114 AC: 17209 AN: 151234 Hom.: 1613 Cov.: 31

Gnomad AFR AF: 0.0680

Gnomad AMI AF: 0.0319

Gnomad AMR AF: 0.158

Gnomad ASJ AF: 0.123

Gnomad EAS AF: 0.538

Gnomad SAS AF: 0.223

Gnomad FIN AF: 0.116

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.0915

Gnomad OTH AF: 0.130

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

GnomAD4 genome AF: 0.114 AC: 17214 AN: 151354 Hom.: 1612 Cov.: 31 AF XY: 0.121 AC XY: 8980 AN XY: 73918

Gnomad4 AFR AF: 0.0679

Gnomad4 AMR AF: 0.158

Gnomad4 ASJ AF: 0.123

Gnomad4 EAS AF: 0.538

Gnomad4 SAS AF: 0.223

Gnomad4 FIN AF: 0.116

Gnomad4 NFE AF: 0.0915

Gnomad4 OTH AF: 0.129

Alfa AF: 0.111 Hom.: 2887

Bravo AF: 0.117

Asia WGS AF: 0.321 AC: 1116 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	1.8
Dann	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11241713; hg19: chr5-123119565;