7-119318926-T-G

Variant names:

• chr7-119318926-T-G
• rs308143

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 0.854 in 152,028 control chromosomes in the GnomAD database, including 58,347 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 0.85 (58347 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.272
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.982 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: 0.855 AC: 129851 AN: 151910 Hom.: 58343 Cov.: 33

Gnomad AFR AF: 0.545

Gnomad AMI AF: 0.989

Gnomad AMR AF: 0.909

Gnomad ASJ AF: 0.996

Gnomad EAS AF: 0.902

Gnomad SAS AF: 0.971

Gnomad FIN AF: 0.985

Gnomad MID AF: 0.962

Gnomad NFE AF: 0.988

Gnomad OTH AF: 0.888

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

GnomAD4 genome AF: 0.854 AC: 129888 AN: 152028 Hom.: 58347 Cov.: 33 AF XY: 0.859 AC XY: 63828 AN XY: 74332

African (AFR) AF: 0.544 AC: 22547 AN: 41434

American (AMR) AF: 0.909 AC: 13843 AN: 15222

Ashkenazi Jewish (ASJ) AF: 0.996 AC: 3457 AN: 3470

East Asian (EAS) AF: 0.902 AC: 4668 AN: 5178

South Asian (SAS) AF: 0.972 AC: 4689 AN: 4826

European-Finnish (FIN) AF: 0.985 AC: 10456 AN: 10618

Middle Eastern (MID) AF: 0.959 AC: 282 AN: 294

European-Non Finnish (NFE) AF: 0.988 AC: 67178 AN: 67964

Other (OTH) AF: 0.884 AC: 1866 AN: 2110

Alfa AF: 0.955 Hom.: 27697

Bravo AF: 0.833

Asia WGS AF: 0.875 AC: 3030 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.60
DANN	Benign	0.60
PhyloP100		-0.27

Splicing

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

Other links and lift over

dbSNP: rs308143; hg19: chr7-118958980;