11-4521622-C-T

Variant names:

• chr11-4521622-C-T
• rs10500605

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 0.0803 in 151,782 control chromosomes in the GnomAD database, including 1,068 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 0.080 (1068 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.276
• Publications: 1 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 (AFR) allele frequency at 95% confidence interval = 0.201 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: 0.0801 AC: 12142 AN: 151664 Hom.: 1063 Cov.: 32

Gnomad AFR AF: 0.205

Gnomad AMI AF: 0.0439

Gnomad AMR AF: 0.0455

Gnomad ASJ AF: 0.0566

Gnomad EAS AF: 0.0441

Gnomad SAS AF: 0.0203

Gnomad FIN AF: 0.0110

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0324

Gnomad OTH AF: 0.0714

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

GnomAD4 genome AF: 0.0803 AC: 12183 AN: 151782 Hom.: 1068 Cov.: 32 AF XY: 0.0778 AC XY: 5769 AN XY: 74170

African (AFR) AF: 0.205 AC: 8434 AN: 41164

American (AMR) AF: 0.0454 AC: 692 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.0566 AC: 196 AN: 3464

East Asian (EAS) AF: 0.0438 AC: 227 AN: 5184

South Asian (SAS) AF: 0.0205 AC: 99 AN: 4818

European-Finnish (FIN) AF: 0.0110 AC: 116 AN: 10564

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.0324 AC: 2201 AN: 68020

Other (OTH) AF: 0.0731 AC: 154 AN: 2108

Alfa AF: 0.00707 Hom.: 5

Bravo AF: 0.0878

Asia WGS AF: 0.0570 AC: 198 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	6.7
DANN	Benign	0.47
PhyloP100		0.28

Splicing

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

Other links and lift over

dbSNP: rs10500605; hg19: chr11-4542852;