7-116937070-G-A

Variant names:

• chr7-116937070-G-A
• rs7782376

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 0.298 in 151,958 control chromosomes in the GnomAD database, including 8,744 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 0.30 (8744 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.48
• Publications: 17 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.528 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.298 AC: 45262 AN: 151836 Hom.: 8740 Cov.: 32

Gnomad AFR AF: 0.523

Gnomad AMI AF: 0.148

Gnomad AMR AF: 0.250

Gnomad ASJ AF: 0.280

Gnomad EAS AF: 0.545

Gnomad SAS AF: 0.316

Gnomad FIN AF: 0.254

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.163

Gnomad OTH AF: 0.274

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

GnomAD4 genome AF: 0.298 AC: 45307 AN: 151958 Hom.: 8744 Cov.: 32 AF XY: 0.304 AC XY: 22562 AN XY: 74238

African (AFR) AF: 0.523 AC: 21646 AN: 41424

American (AMR) AF: 0.250 AC: 3819 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.280 AC: 970 AN: 3462

East Asian (EAS) AF: 0.545 AC: 2801 AN: 5142

South Asian (SAS) AF: 0.315 AC: 1512 AN: 4804

European-Finnish (FIN) AF: 0.254 AC: 2677 AN: 10556

Middle Eastern (MID) AF: 0.228 AC: 67 AN: 294

European-Non Finnish (NFE) AF: 0.163 AC: 11093 AN: 67988

Other (OTH) AF: 0.278 AC: 587 AN: 2112

Alfa AF: 0.214 Hom.: 17610

Bravo AF: 0.311

Asia WGS AF: 0.439 AC: 1527 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.17
DANN	Benign	0.31
PhyloP100		-2.5

Splicing

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

Other links and lift over

dbSNP: rs7782376; hg19: chr7-116577124;