rs4910722

Positions:

• chr11-5175487-G-A
• chr11-5175487-G-C
• chr11-5175487-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 0.935 in 152,180 control chromosomes in the GnomAD database, including 66,896 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 0.93 (66896 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.09

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.977 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.935 AC: 142182 AN: 152062 Hom.: 66864 Cov.: 30

Gnomad AFR AF: 0.828

Gnomad AMI AF: 0.980

Gnomad AMR AF: 0.977

Gnomad ASJ AF: 0.981

Gnomad EAS AF: 0.935

Gnomad SAS AF: 0.881

Gnomad FIN AF: 0.986

Gnomad MID AF: 0.965

Gnomad NFE AF: 0.983

Gnomad OTH AF: 0.945

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

GnomAD4 genome AF: 0.935 AC: 142268 AN: 152180 Hom.: 66896 Cov.: 30 AF XY: 0.934 AC XY: 69524 AN XY: 74430

Gnomad4 AFR AF: 0.827

Gnomad4 AMR AF: 0.977

Gnomad4 ASJ AF: 0.981

Gnomad4 EAS AF: 0.936

Gnomad4 SAS AF: 0.880

Gnomad4 FIN AF: 0.986

Gnomad4 NFE AF: 0.983

Gnomad4 OTH AF: 0.946

Alfa AF: 0.940 Hom.: 9188

Bravo AF: 0.932

Asia WGS AF: 0.913 AC: 3175 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.35
DANN	Benign	0.67

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs4910722; hg19: chr11-5196717;