11-69634495-G-T

Variant names:

• chr11-69634495-G-T
• rs1683847

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 0.5 in 152,058 control chromosomes in the GnomAD database, including 21,013 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 0.50 (21013 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.42
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.727 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.500 AC: 75982 AN: 151940 Hom.: 20969 Cov.: 33

Gnomad AFR AF: 0.734

Gnomad AMI AF: 0.492

Gnomad AMR AF: 0.542

Gnomad ASJ AF: 0.407

Gnomad EAS AF: 0.173

Gnomad SAS AF: 0.366

Gnomad FIN AF: 0.366

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.410

Gnomad OTH AF: 0.482

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

GnomAD4 genome AF: 0.500 AC: 76083 AN: 152058 Hom.: 21013 Cov.: 33 AF XY: 0.495 AC XY: 36784 AN XY: 74332

African (AFR) AF: 0.734 AC: 30439 AN: 41474

American (AMR) AF: 0.542 AC: 8292 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.407 AC: 1412 AN: 3468

East Asian (EAS) AF: 0.172 AC: 889 AN: 5156

South Asian (SAS) AF: 0.365 AC: 1759 AN: 4824

European-Finnish (FIN) AF: 0.366 AC: 3874 AN: 10582

Middle Eastern (MID) AF: 0.449 AC: 132 AN: 294

European-Non Finnish (NFE) AF: 0.410 AC: 27830 AN: 67950

Other (OTH) AF: 0.479 AC: 1009 AN: 2108

Alfa AF: 0.390 Hom.: 2361

Bravo AF: 0.525

Asia WGS AF: 0.333 AC: 1161 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.085
DANN	Benign	0.32
PhyloP100		-3.4

Splicing

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

Other links and lift over

dbSNP: rs1683847; hg19: chr11-69449263;