11-69634495-G-T

Variant names:

• chr11-69634495-G-T
• rs1683847

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.500 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

Gnomad4 AFR AF: 0.734

Gnomad4 AMR AF: 0.542

Gnomad4 ASJ AF: 0.407

Gnomad4 EAS AF: 0.172

Gnomad4 SAS AF: 0.365

Gnomad4 FIN AF: 0.366

Gnomad4 NFE AF: 0.410

Gnomad4 OTH AF: 0.479

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1683847; hg19: chr11-69449263;