rs734102

Variant names:

• chr11-69809714-C-T
• rs734102

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 0.0985 in 152,090 control chromosomes in the GnomAD database, including 790 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 0.099 (790 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.555
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.113 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.0985 AC: 14974 AN: 151972 Hom.: 792 Cov.: 33

Gnomad AFR AF: 0.116

Gnomad AMI AF: 0.0789

Gnomad AMR AF: 0.0511

Gnomad ASJ AF: 0.0380

Gnomad EAS AF: 0.0158

Gnomad SAS AF: 0.0902

Gnomad FIN AF: 0.110

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.108

Gnomad OTH AF: 0.0883

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

GnomAD4 genome AF: 0.0985 AC: 14981 AN: 152090 Hom.: 790 Cov.: 33 AF XY: 0.0980 AC XY: 7291 AN XY: 74362

African (AFR) AF: 0.116 AC: 4805 AN: 41480

American (AMR) AF: 0.0510 AC: 780 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0380 AC: 132 AN: 3472

East Asian (EAS) AF: 0.0159 AC: 82 AN: 5166

South Asian (SAS) AF: 0.0907 AC: 438 AN: 4830

European-Finnish (FIN) AF: 0.110 AC: 1160 AN: 10588

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.108 AC: 7315 AN: 67960

Other (OTH) AF: 0.0874 AC: 184 AN: 2106

Alfa AF: 0.101 Hom.: 1081

Bravo AF: 0.0934

Asia WGS AF: 0.0570 AC: 200 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	8.2
DANN	Benign	0.82
PhyloP100		0.56

Splicing

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

Other links and lift over

dbSNP: rs734102; hg19: chr11-69624482;