11-40019740-A-G

Variant names:

• chr11-40019740-A-G
• rs6485172

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 0.782 in 152,106 control chromosomes in the GnomAD database, including 47,054 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 0.78 (47054 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.677
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.845 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: 0.782 AC: 118799 AN: 151988 Hom.: 47012 Cov.: 32

Gnomad AFR AF: 0.667

Gnomad AMI AF: 0.862

Gnomad AMR AF: 0.792

Gnomad ASJ AF: 0.870

Gnomad EAS AF: 0.624

Gnomad SAS AF: 0.850

Gnomad FIN AF: 0.778

Gnomad MID AF: 0.839

Gnomad NFE AF: 0.851

Gnomad OTH AF: 0.793

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

GnomAD4 genome AF: 0.782 AC: 118903 AN: 152106 Hom.: 47054 Cov.: 32 AF XY: 0.779 AC XY: 57913 AN XY: 74338

African (AFR) AF: 0.667 AC: 27666 AN: 41472

American (AMR) AF: 0.792 AC: 12105 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.870 AC: 3015 AN: 3466

East Asian (EAS) AF: 0.624 AC: 3226 AN: 5168

South Asian (SAS) AF: 0.850 AC: 4099 AN: 4824

European-Finnish (FIN) AF: 0.778 AC: 8226 AN: 10580

Middle Eastern (MID) AF: 0.844 AC: 248 AN: 294

European-Non Finnish (NFE) AF: 0.851 AC: 57853 AN: 68002

Other (OTH) AF: 0.795 AC: 1679 AN: 2112

Alfa AF: 0.832 Hom.: 225122

Bravo AF: 0.777

Asia WGS AF: 0.747 AC: 2598 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	9.1
DANN	Benign	0.74
PhyloP100		0.68

Splicing

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

Other links and lift over

dbSNP: rs6485172; hg19: chr11-40041290;