rs11749751

Variant names:

• chr5-108565853-G-A
• rs11749751

Your query was ambiguous. Multiple possible variants found:

• chr5-108565853-G-A
• chr5-108565853-G-C
• chr5-108565853-G-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 0.822 in 152,206 control chromosomes in the GnomAD database, including 52,141 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 0.82 (52141 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.287

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.948 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: 0.822 AC: 125005 AN: 152088 Hom.: 52098 Cov.: 32

Gnomad AFR AF: 0.956

Gnomad AMI AF: 0.859

Gnomad AMR AF: 0.726

Gnomad ASJ AF: 0.781

Gnomad EAS AF: 0.607

Gnomad SAS AF: 0.667

Gnomad FIN AF: 0.831

Gnomad MID AF: 0.764

Gnomad NFE AF: 0.790

Gnomad OTH AF: 0.795

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

GnomAD4 genome AF: 0.822 AC: 125092 AN: 152206 Hom.: 52141 Cov.: 32 AF XY: 0.818 AC XY: 60868 AN XY: 74418

Gnomad4 AFR AF: 0.956

Gnomad4 AMR AF: 0.725

Gnomad4 ASJ AF: 0.781

Gnomad4 EAS AF: 0.607

Gnomad4 SAS AF: 0.667

Gnomad4 FIN AF: 0.831

Gnomad4 NFE AF: 0.790

Gnomad4 OTH AF: 0.790

Alfa AF: 0.798 Hom.: 44622

Bravo AF: 0.821

Asia WGS AF: 0.680 AC: 2367 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.6
DANN	Benign	0.20

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11749751; hg19: chr5-107901554; COSMIC: COSV60180645;