11-29140589-T-C

Variant names:

• chr11-29140589-T-C
• rs1602565

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 0.0996 in 151,948 control chromosomes in the GnomAD database, including 934 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 0.10 (934 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0490
• Publications: 19 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.165 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: 0.0996 AC: 15123 AN: 151832 Hom.: 927 Cov.: 31

Gnomad AFR AF: 0.0367

Gnomad AMI AF: 0.207

Gnomad AMR AF: 0.171

Gnomad ASJ AF: 0.171

Gnomad EAS AF: 0.146

Gnomad SAS AF: 0.141

Gnomad FIN AF: 0.0839

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.112

Gnomad OTH AF: 0.115

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

GnomAD4 genome AF: 0.0996 AC: 15139 AN: 151948 Hom.: 934 Cov.: 31 AF XY: 0.100 AC XY: 7442 AN XY: 74228

African (AFR) AF: 0.0367 AC: 1523 AN: 41536

American (AMR) AF: 0.171 AC: 2596 AN: 15192

Ashkenazi Jewish (ASJ) AF: 0.171 AC: 592 AN: 3464

East Asian (EAS) AF: 0.146 AC: 751 AN: 5130

South Asian (SAS) AF: 0.140 AC: 675 AN: 4826

European-Finnish (FIN) AF: 0.0839 AC: 889 AN: 10592

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.112 AC: 7635 AN: 67896

Other (OTH) AF: 0.118 AC: 249 AN: 2106

Alfa AF: 0.114 Hom.: 2411

Bravo AF: 0.104

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	3.2
DANN	Benign	0.75
PhyloP100		-0.049

Splicing

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

Other links and lift over

dbSNP: rs1602565; hg19: chr11-29162136;