rs575341

Variant names:

• chr11-72146329-T-C
• rs575341

Your query was ambiguous. Multiple possible variants found:

• chr11-72146329-T-C
• chr11-72146329-T-G

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 0.814 in 152,016 control chromosomes in the GnomAD database, including 51,130 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 0.81 (51130 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.284
• Publications: 13 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.879 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: 0.814 AC: 123629 AN: 151898 Hom.: 51086 Cov.: 30

Gnomad AFR AF: 0.655

Gnomad AMI AF: 0.970

Gnomad AMR AF: 0.891

Gnomad ASJ AF: 0.869

Gnomad EAS AF: 0.775

Gnomad SAS AF: 0.827

Gnomad FIN AF: 0.854

Gnomad MID AF: 0.870

Gnomad NFE AF: 0.883

Gnomad OTH AF: 0.835

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

GnomAD4 genome AF: 0.814 AC: 123724 AN: 152016 Hom.: 51130 Cov.: 30 AF XY: 0.812 AC XY: 60334 AN XY: 74292

African (AFR) AF: 0.656 AC: 27141 AN: 41404

American (AMR) AF: 0.892 AC: 13626 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.869 AC: 3016 AN: 3470

East Asian (EAS) AF: 0.775 AC: 3998 AN: 5156

South Asian (SAS) AF: 0.827 AC: 3982 AN: 4814

European-Finnish (FIN) AF: 0.854 AC: 9028 AN: 10570

Middle Eastern (MID) AF: 0.874 AC: 257 AN: 294

European-Non Finnish (NFE) AF: 0.883 AC: 60032 AN: 68006

Other (OTH) AF: 0.834 AC: 1759 AN: 2108

Alfa AF: 0.837 Hom.: 8801

Bravo AF: 0.810

Asia WGS AF: 0.777 AC: 2703 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	6.1
DANN	Benign	0.70
PhyloP100		0.28

Splicing

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

Other links and lift over

dbSNP: rs575341; hg19: chr11-71857373;