rs11241713

Variant names:

• chr5-123783871-C-A
• rs11241713

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 10 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.0679 AC: 2804 AN: 41290

American (AMR) AF: 0.158 AC: 2405 AN: 15174

Ashkenazi Jewish (ASJ) AF: 0.123 AC: 426 AN: 3462

East Asian (EAS) AF: 0.538 AC: 2750 AN: 5112

South Asian (SAS) AF: 0.223 AC: 1070 AN: 4792

European-Finnish (FIN) AF: 0.116 AC: 1209 AN: 10400

Middle Eastern (MID) AF: 0.144 AC: 42 AN: 292

European-Non Finnish (NFE) AF: 0.0915 AC: 6209 AN: 67826

Other (OTH) AF: 0.129 AC: 270 AN: 2096

Alfa AF: 0.111 Hom.: 4114

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
PhyloP100		-0.025

Splicing

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

Other links and lift over

dbSNP: rs11241713; hg19: chr5-123119565;