7-138364642-C-G

Variant names:

• chr7-138364642-C-G
• rs357394

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 0.876 in 152,100 control chromosomes in the GnomAD database, including 58,484 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 0.88 (58484 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.798
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.956 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: 0.876 AC: 133167 AN: 151982 Hom.: 58438 Cov.: 30

Gnomad AFR AF: 0.910

Gnomad AMI AF: 0.940

Gnomad AMR AF: 0.785

Gnomad ASJ AF: 0.863

Gnomad EAS AF: 0.978

Gnomad SAS AF: 0.875

Gnomad FIN AF: 0.894

Gnomad MID AF: 0.886

Gnomad NFE AF: 0.866

Gnomad OTH AF: 0.868

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

GnomAD4 genome AF: 0.876 AC: 133275 AN: 152100 Hom.: 58484 Cov.: 30 AF XY: 0.876 AC XY: 65137 AN XY: 74354

African (AFR) AF: 0.910 AC: 37748 AN: 41496

American (AMR) AF: 0.785 AC: 11947 AN: 15228

Ashkenazi Jewish (ASJ) AF: 0.863 AC: 2995 AN: 3472

East Asian (EAS) AF: 0.978 AC: 5058 AN: 5170

South Asian (SAS) AF: 0.876 AC: 4222 AN: 4818

European-Finnish (FIN) AF: 0.894 AC: 9475 AN: 10594

Middle Eastern (MID) AF: 0.884 AC: 260 AN: 294

European-Non Finnish (NFE) AF: 0.866 AC: 58873 AN: 68000

Other (OTH) AF: 0.870 AC: 1840 AN: 2116

Alfa AF: 0.864 Hom.: 2789

Bravo AF: 0.870

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.84
DANN	Benign	0.19
PhyloP100		-0.80

Splicing

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

Other links and lift over

dbSNP: rs357394; hg19: chr7-138049387;