7-9027190-C-T

Variant names:

• chr7-9027190-C-T
• rs10952132

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.221 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

Gnomad4 AFR AF: 0.276

Gnomad4 AMR AF: 0.217

Gnomad4 ASJ AF: 0.215

Gnomad4 EAS AF: 0.126

Gnomad4 SAS AF: 0.218

Gnomad4 FIN AF: 0.228

Gnomad4 NFE AF: 0.195

Gnomad4 OTH AF: 0.239

Alfa AF: 0.190 Hom.: 4054

Bravo AF: 0.223

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10952132; hg19: chr7-9066820;