11-116715567-T-C

Variant names:

• chr11-116715567-T-C
• rs7350481

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 0.928 in 152,010 control chromosomes in the GnomAD database, including 65,756 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 0.93 (65756 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.341
• Publications: 43 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.978 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: 0.928 AC: 140996 AN: 151892 Hom.: 65708 Cov.: 28

Gnomad AFR AF: 0.986

Gnomad AMI AF: 0.900

Gnomad AMR AF: 0.875

Gnomad ASJ AF: 0.908

Gnomad EAS AF: 0.750

Gnomad SAS AF: 0.778

Gnomad FIN AF: 0.923

Gnomad MID AF: 0.848

Gnomad NFE AF: 0.933

Gnomad OTH AF: 0.909

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

GnomAD4 genome AF: 0.928 AC: 141102 AN: 152010 Hom.: 65756 Cov.: 28 AF XY: 0.923 AC XY: 68568 AN XY: 74304

African (AFR) AF: 0.986 AC: 40879 AN: 41474

American (AMR) AF: 0.875 AC: 13350 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.908 AC: 3151 AN: 3472

East Asian (EAS) AF: 0.749 AC: 3822 AN: 5106

South Asian (SAS) AF: 0.778 AC: 3730 AN: 4796

European-Finnish (FIN) AF: 0.923 AC: 9766 AN: 10580

Middle Eastern (MID) AF: 0.847 AC: 249 AN: 294

European-Non Finnish (NFE) AF: 0.933 AC: 63421 AN: 68000

Other (OTH) AF: 0.905 AC: 1913 AN: 2114

Alfa AF: 0.924 Hom.: 235778

Bravo AF: 0.928

Asia WGS AF: 0.779 AC: 2710 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.93
DANN	Benign	0.49
PhyloP100		-0.34

Splicing

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

Other links and lift over

dbSNP: rs7350481; hg19: chr11-116586283;