rs2882834

chr7-10325096-C-Gchr7-10325096-C-T

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 0.305 in 151,914 control chromosomes in the GnomAD database, including 7,730 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 0.30 (7730 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.450

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.372 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.305 AC: 46259 AN: 151796 Hom.: 7723 Cov.: 31

Gnomad AFR AF: 0.198

Gnomad AMI AF: 0.226

Gnomad AMR AF: 0.355

Gnomad ASJ AF: 0.330

Gnomad EAS AF: 0.0530

Gnomad SAS AF: 0.221

Gnomad FIN AF: 0.348

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.376

Gnomad OTH AF: 0.319

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

GnomAD4 genome AF: 0.305 AC: 46290 AN: 151914 Hom.: 7730 Cov.: 31 AF XY: 0.297 AC XY: 22046 AN XY: 74246

Gnomad4 AFR AF: 0.198

Gnomad4 AMR AF: 0.355

Gnomad4 ASJ AF: 0.330

Gnomad4 EAS AF: 0.0531

Gnomad4 SAS AF: 0.221

Gnomad4 FIN AF: 0.348

Gnomad4 NFE AF: 0.376

Gnomad4 OTH AF: 0.320

Alfa AF: 0.212 Hom.: 526

Bravo AF: 0.300

Asia WGS AF: 0.204 AC: 712 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	1.0
Dann	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2882834; hg19: chr7-10364723;