rs11564750

Variant names:

• chr5-1447647-G-C
• rs11564750

Your query was ambiguous. Multiple possible variants found:

• chr5-1447647-G-C
• chr5-1447647-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 0.065 in 152,276 control chromosomes in the GnomAD database, including 431 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 0.065 (431 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.232

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0938 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: 0.0651 AC: 9899 AN: 152158 Hom.: 431 Cov.: 33

Gnomad AFR AF: 0.0255

Gnomad AMI AF: 0.102

Gnomad AMR AF: 0.0335

Gnomad ASJ AF: 0.0242

Gnomad EAS AF: 0.00173

Gnomad SAS AF: 0.0132

Gnomad FIN AF: 0.138

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0957

Gnomad OTH AF: 0.0502

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

GnomAD4 genome AF: 0.0650 AC: 9900 AN: 152276 Hom.: 431 Cov.: 33 AF XY: 0.0646 AC XY: 4812 AN XY: 74444

Gnomad4 AFR AF: 0.0254

Gnomad4 AMR AF: 0.0335

Gnomad4 ASJ AF: 0.0242

Gnomad4 EAS AF: 0.00173

Gnomad4 SAS AF: 0.0135

Gnomad4 FIN AF: 0.138

Gnomad4 NFE AF: 0.0957

Gnomad4 OTH AF: 0.0492

Alfa AF: 0.0429 Hom.: 34

Bravo AF: 0.0571

Asia WGS AF: 0.0110 AC: 39 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.9
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11564750; hg19: chr5-1447762;