7-9027190-C-T

Variant names:

• chr7-9027190-C-T
• rs10952132

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 0.221 in 151,960 control chromosomes in the GnomAD database, including 3,835 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 0.22 (3835 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.560
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.271 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: 0.221 AC: 33505 AN: 151842 Hom.: 3827 Cov.: 33

Gnomad AFR AF: 0.275

Gnomad AMI AF: 0.149

Gnomad AMR AF: 0.217

Gnomad ASJ AF: 0.215

Gnomad EAS AF: 0.126

Gnomad SAS AF: 0.217

Gnomad FIN AF: 0.228

Gnomad MID AF: 0.242

Gnomad NFE AF: 0.195

Gnomad OTH AF: 0.236

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

GnomAD4 genome AF: 0.221 AC: 33553 AN: 151960 Hom.: 3835 Cov.: 33 AF XY: 0.223 AC XY: 16585 AN XY: 74258

African (AFR) AF: 0.276 AC: 11432 AN: 41478

American (AMR) AF: 0.217 AC: 3301 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.215 AC: 747 AN: 3468

East Asian (EAS) AF: 0.126 AC: 648 AN: 5154

South Asian (SAS) AF: 0.218 AC: 1051 AN: 4820

European-Finnish (FIN) AF: 0.228 AC: 2404 AN: 10554

Middle Eastern (MID) AF: 0.247 AC: 72 AN: 292

European-Non Finnish (NFE) AF: 0.195 AC: 13258 AN: 67938

Other (OTH) AF: 0.239 AC: 504 AN: 2106

Alfa AF: 0.198 Hom.: 9756

Bravo AF: 0.223

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.6
DANN	Benign	0.76
PhyloP100		-0.56

Splicing

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

Other links and lift over

dbSNP: rs10952132; hg19: chr7-9066820;