11-102534940-A-T

Variant names:

• chr11-102534940-A-T
• rs880197

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 0.799 in 152,154 control chromosomes in the GnomAD database, including 49,065 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 0.80 (49065 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.234
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.886 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: 0.799 AC: 121495 AN: 152034 Hom.: 49005 Cov.: 31

Gnomad AFR AF: 0.893

Gnomad AMI AF: 0.851

Gnomad AMR AF: 0.725

Gnomad ASJ AF: 0.821

Gnomad EAS AF: 0.609

Gnomad SAS AF: 0.737

Gnomad FIN AF: 0.755

Gnomad MID AF: 0.876

Gnomad NFE AF: 0.782

Gnomad OTH AF: 0.802

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

GnomAD4 genome AF: 0.799 AC: 121617 AN: 152154 Hom.: 49065 Cov.: 31 AF XY: 0.795 AC XY: 59160 AN XY: 74396

African (AFR) AF: 0.894 AC: 37108 AN: 41520

American (AMR) AF: 0.726 AC: 11096 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.821 AC: 2852 AN: 3472

East Asian (EAS) AF: 0.609 AC: 3147 AN: 5164

South Asian (SAS) AF: 0.737 AC: 3547 AN: 4812

European-Finnish (FIN) AF: 0.755 AC: 7987 AN: 10572

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

European-Non Finnish (NFE) AF: 0.782 AC: 53155 AN: 68000

Other (OTH) AF: 0.800 AC: 1692 AN: 2116

Alfa AF: 0.796 Hom.: 6000

Bravo AF: 0.802

Asia WGS AF: 0.709 AC: 2468 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.77
DANN	Benign	0.63
PhyloP100		-0.23

Splicing

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

Other links and lift over

dbSNP: rs880197; hg19: chr11-102405671;