rs916598

Variant names:

• chr7-127286837-A-G
• rs916598

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 0.574 in 152,200 control chromosomes in the GnomAD database, including 28,090 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 (28090 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.400
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.857 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: 0.574 AC: 87231 AN: 152080 Hom.: 28049 Cov.: 33

Gnomad AFR AF: 0.864

Gnomad AMI AF: 0.566

Gnomad AMR AF: 0.483

Gnomad ASJ AF: 0.694

Gnomad EAS AF: 0.166

Gnomad SAS AF: 0.377

Gnomad FIN AF: 0.389

Gnomad MID AF: 0.703

Gnomad NFE AF: 0.484

Gnomad OTH AF: 0.584

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

GnomAD4 genome AF: 0.574 AC: 87311 AN: 152200 Hom.: 28090 Cov.: 33 AF XY: 0.561 AC XY: 41768 AN XY: 74408

African (AFR) AF: 0.864 AC: 35895 AN: 41536

American (AMR) AF: 0.482 AC: 7361 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.694 AC: 2408 AN: 3470

East Asian (EAS) AF: 0.166 AC: 859 AN: 5184

South Asian (SAS) AF: 0.375 AC: 1808 AN: 4820

European-Finnish (FIN) AF: 0.389 AC: 4129 AN: 10602

Middle Eastern (MID) AF: 0.694 AC: 204 AN: 294

European-Non Finnish (NFE) AF: 0.484 AC: 32911 AN: 67994

Other (OTH) AF: 0.579 AC: 1221 AN: 2108

Alfa AF: 0.516 Hom.: 94435

Bravo AF: 0.595

Asia WGS AF: 0.321 AC: 1118 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.1
DANN	Benign	0.79
PhyloP100		0.40

Splicing

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

Other links and lift over

dbSNP: rs916598; hg19: chr7-126926891;