7-117874786-T-G

Variant names:

• chr7-117874786-T-G
• rs6965740

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.657

Gnomad4 AMR AF: 0.443

Gnomad4 ASJ AF: 0.489

Gnomad4 EAS AF: 0.407

Gnomad4 SAS AF: 0.518

Gnomad4 FIN AF: 0.636

Gnomad4 NFE AF: 0.565

Gnomad4 OTH AF: 0.518

Alfa AF: 0.553 Hom.: 12187

Bravo AF: 0.558

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6965740; hg19: chr7-117514840;