7-117874786-T-G

Variant names:

• chr7-117874786-T-G
• rs6965740

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.571 in 148,132 control chromosomes in the GnomAD database, including 24,805 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 0.57 (24805 hom., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.13
• Publications: 9 publications found

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.37).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.65 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: 0.571 AC: 84567 AN: 148022 Hom.: 24782 Cov.: 23

Gnomad AFR AF: 0.657

Gnomad AMI AF: 0.343

Gnomad AMR AF: 0.443

Gnomad ASJ AF: 0.489

Gnomad EAS AF: 0.407

Gnomad SAS AF: 0.519

Gnomad FIN AF: 0.636

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.565

Gnomad OTH AF: 0.521

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

GnomAD4 genome AF: 0.571 AC: 84634 AN: 148132 Hom.: 24805 Cov.: 23 AF XY: 0.573 AC XY: 41251 AN XY: 72034

African (AFR) AF: 0.657 AC: 26164 AN: 39822

American (AMR) AF: 0.443 AC: 6570 AN: 14828

Ashkenazi Jewish (ASJ) AF: 0.489 AC: 1691 AN: 3456

East Asian (EAS) AF: 0.407 AC: 2041 AN: 5010

South Asian (SAS) AF: 0.518 AC: 2406 AN: 4642

European-Finnish (FIN) AF: 0.636 AC: 6106 AN: 9606

Middle Eastern (MID) AF: 0.476 AC: 137 AN: 288

European-Non Finnish (NFE) AF: 0.565 AC: 38148 AN: 67528

Other (OTH) AF: 0.518 AC: 1062 AN: 2052

Alfa AF: 0.552 Hom.: 17249

Bravo AF: 0.558

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.37
CADD	Benign	16
DANN	Benign	0.79
PhyloP100		2.1

Splicing

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

Other links and lift over

dbSNP: rs6965740; hg19: chr7-117514840;