7-130291562-G-T

Variant names:

• chr7-130291562-G-T
• rs901799

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 0.141 in 152,196 control chromosomes in the GnomAD database, including 1,661 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 0.14 (1661 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.395
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.164 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: 0.141 AC: 21415 AN: 152078 Hom.: 1661 Cov.: 31

Gnomad AFR AF: 0.105

Gnomad AMI AF: 0.242

Gnomad AMR AF: 0.145

Gnomad ASJ AF: 0.172

Gnomad EAS AF: 0.143

Gnomad SAS AF: 0.143

Gnomad FIN AF: 0.0842

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.167

Gnomad OTH AF: 0.160

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

GnomAD4 genome AF: 0.141 AC: 21419 AN: 152196 Hom.: 1661 Cov.: 31 AF XY: 0.138 AC XY: 10279 AN XY: 74408

African (AFR) AF: 0.105 AC: 4365 AN: 41522

American (AMR) AF: 0.145 AC: 2218 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.172 AC: 597 AN: 3470

East Asian (EAS) AF: 0.142 AC: 734 AN: 5170

South Asian (SAS) AF: 0.142 AC: 686 AN: 4824

European-Finnish (FIN) AF: 0.0842 AC: 893 AN: 10608

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.167 AC: 11332 AN: 68000

Other (OTH) AF: 0.159 AC: 336 AN: 2110

Alfa AF: 0.158 Hom.: 3470

Bravo AF: 0.143

Asia WGS AF: 0.139 AC: 482 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.3
DANN	Benign	0.64
PhyloP100		0.40

Splicing

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

Other links and lift over

dbSNP: rs901799; hg19: chr7-129931402;