7-116511730-G-C

Variant names:

• chr7-116511730-G-C
• rs3919515

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 0.492 in 152,072 control chromosomes in the GnomAD database, including 18,976 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 0.49 (18976 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.156
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.754 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: 0.492 AC: 74695 AN: 151954 Hom.: 18954 Cov.: 32

Gnomad AFR AF: 0.392

Gnomad AMI AF: 0.424

Gnomad AMR AF: 0.560

Gnomad ASJ AF: 0.486

Gnomad EAS AF: 0.775

Gnomad SAS AF: 0.548

Gnomad FIN AF: 0.566

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.501

Gnomad OTH AF: 0.498

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

GnomAD4 genome AF: 0.492 AC: 74759 AN: 152072 Hom.: 18976 Cov.: 32 AF XY: 0.500 AC XY: 37136 AN XY: 74316

African (AFR) AF: 0.392 AC: 16239 AN: 41476

American (AMR) AF: 0.561 AC: 8572 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.486 AC: 1685 AN: 3468

East Asian (EAS) AF: 0.774 AC: 4004 AN: 5170

South Asian (SAS) AF: 0.548 AC: 2641 AN: 4818

European-Finnish (FIN) AF: 0.566 AC: 5975 AN: 10558

Middle Eastern (MID) AF: 0.449 AC: 132 AN: 294

European-Non Finnish (NFE) AF: 0.501 AC: 34064 AN: 67984

Other (OTH) AF: 0.502 AC: 1060 AN: 2112

Alfa AF: 0.510 Hom.: 2486

Bravo AF: 0.484

Asia WGS AF: 0.680 AC: 2359 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	5.3
DANN	Benign	0.57
PhyloP100		-0.16

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs3919515;

hg19: chr7-116151784;