rs11070396

Variant names:

• chr15-43230724-C-A
• rs11070396

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 0.125 in 152,220 control chromosomes in the GnomAD database, including 1,336 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 0.12 (1336 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.380
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.66).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.2 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: 0.125 AC: 18939 AN: 152102 Hom.: 1330 Cov.: 32

Gnomad AFR AF: 0.180

Gnomad AMI AF: 0.0954

Gnomad AMR AF: 0.124

Gnomad ASJ AF: 0.0753

Gnomad EAS AF: 0.211

Gnomad SAS AF: 0.115

Gnomad FIN AF: 0.0949

Gnomad MID AF: 0.0764

Gnomad NFE AF: 0.0932

Gnomad OTH AF: 0.112

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

GnomAD4 genome AF: 0.125 AC: 18977 AN: 152220 Hom.: 1336 Cov.: 32 AF XY: 0.126 AC XY: 9370 AN XY: 74434

African (AFR) AF: 0.180 AC: 7476 AN: 41518

American (AMR) AF: 0.124 AC: 1894 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0753 AC: 261 AN: 3468

East Asian (EAS) AF: 0.211 AC: 1089 AN: 5172

South Asian (SAS) AF: 0.115 AC: 555 AN: 4826

European-Finnish (FIN) AF: 0.0949 AC: 1007 AN: 10608

Middle Eastern (MID) AF: 0.0822 AC: 24 AN: 292

European-Non Finnish (NFE) AF: 0.0931 AC: 6335 AN: 68016

Other (OTH) AF: 0.118 AC: 249 AN: 2110

Alfa AF: 0.103 Hom.: 1573

Bravo AF: 0.132

Asia WGS AF: 0.172 AC: 600 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	2.3
DANN	Benign	0.83
PhyloP100		-0.38

Splicing

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

Other links and lift over

dbSNP: rs11070396; hg19: chr15-43522922;