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. The variant received -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
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.956 AC: 39735 AN: 41554

American (AMR) AF: 0.725 AC: 11083 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.781 AC: 2711 AN: 3470

East Asian (EAS) AF: 0.607 AC: 3136 AN: 5170

South Asian (SAS) AF: 0.667 AC: 3215 AN: 4820

European-Finnish (FIN) AF: 0.831 AC: 8804 AN: 10596

Middle Eastern (MID) AF: 0.753 AC: 220 AN: 292

European-Non Finnish (NFE) AF: 0.790 AC: 53736 AN: 67996

Other (OTH) AF: 0.790 AC: 1669 AN: 2112

Alfa AF: 0.812 Hom.: 73897

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
PhyloP100		0.29

Splicing

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

Other links and lift over

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