rs7394570

Variant names:

• chr11-42294336-A-G
• rs7394570

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 0.896 in 151,974 control chromosomes in the GnomAD database, including 61,975 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 0.90 (61975 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.49
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.06).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 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: 0.896 AC: 136103 AN: 151856 Hom.: 61944 Cov.: 31

Gnomad AFR AF: 0.728

Gnomad AMI AF: 0.989

Gnomad AMR AF: 0.908

Gnomad ASJ AF: 0.986

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.956

Gnomad FIN AF: 0.897

Gnomad MID AF: 0.946

Gnomad NFE AF: 0.977

Gnomad OTH AF: 0.927

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

GnomAD4 genome AF: 0.896 AC: 136192 AN: 151974 Hom.: 61975 Cov.: 31 AF XY: 0.893 AC XY: 66320 AN XY: 74282

African (AFR) AF: 0.728 AC: 30159 AN: 41442

American (AMR) AF: 0.908 AC: 13818 AN: 15220

Ashkenazi Jewish (ASJ) AF: 0.986 AC: 3420 AN: 3468

East Asian (EAS) AF: 0.999 AC: 5150 AN: 5156

South Asian (SAS) AF: 0.955 AC: 4605 AN: 4820

European-Finnish (FIN) AF: 0.897 AC: 9498 AN: 10588

Middle Eastern (MID) AF: 0.942 AC: 277 AN: 294

European-Non Finnish (NFE) AF: 0.977 AC: 66408 AN: 67966

Other (OTH) AF: 0.927 AC: 1955 AN: 2108

Alfa AF: 0.941 Hom.: 132154

Bravo AF: 0.892

Asia WGS AF: 0.961 AC: 3342 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.12
DANN	Benign	0.52
PhyloP100		-2.5

Splicing

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

Other links and lift over

dbSNP: rs7394570; hg19: chr11-42315886;