rs11241713

Variant names:

• chr5-123783871-C-A
• rs11241713

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;