rs916784

Variant names:

• chr7-117959460-A-G
• rs916784

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 0.33 in 152,062 control chromosomes in the GnomAD database, including 9,883 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 0.33 (9883 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0160
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.427 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: 0.330 AC: 50182 AN: 151944 Hom.: 9890 Cov.: 32

Gnomad AFR AF: 0.144

Gnomad AMI AF: 0.228

Gnomad AMR AF: 0.285

Gnomad ASJ AF: 0.358

Gnomad EAS AF: 0.109

Gnomad SAS AF: 0.414

Gnomad FIN AF: 0.550

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.431

Gnomad OTH AF: 0.320

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

GnomAD4 genome AF: 0.330 AC: 50175 AN: 152062 Hom.: 9883 Cov.: 32 AF XY: 0.337 AC XY: 25039 AN XY: 74294

African (AFR) AF: 0.144 AC: 5961 AN: 41536

American (AMR) AF: 0.285 AC: 4347 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.358 AC: 1243 AN: 3470

East Asian (EAS) AF: 0.109 AC: 563 AN: 5180

South Asian (SAS) AF: 0.414 AC: 1990 AN: 4804

European-Finnish (FIN) AF: 0.550 AC: 5790 AN: 10528

Middle Eastern (MID) AF: 0.357 AC: 105 AN: 294

European-Non Finnish (NFE) AF: 0.431 AC: 29302 AN: 67948

Other (OTH) AF: 0.315 AC: 666 AN: 2112

Alfa AF: 0.394 Hom.: 51236

Bravo AF: 0.297

Asia WGS AF: 0.289 AC: 997 AN: 3450

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	3.2
DANN	Benign	0.82
PhyloP100		-0.016

Splicing

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

Other links and lift over

dbSNP: rs916784; hg19: chr7-117599514;