rs10264084

Variant names:

• chr7-150895274-A-T
• rs10264084

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 0.175 in 152,172 control chromosomes in the GnomAD database, including 2,583 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 0.18 (2583 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.493

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.244 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: 0.175 AC: 26649 AN: 152054 Hom.: 2576 Cov.: 32

Gnomad AFR AF: 0.248

Gnomad AMI AF: 0.188

Gnomad AMR AF: 0.131

Gnomad ASJ AF: 0.145

Gnomad EAS AF: 0.0541

Gnomad SAS AF: 0.150

Gnomad FIN AF: 0.134

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.160

Gnomad OTH AF: 0.178

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

GnomAD4 genome AF: 0.175 AC: 26678 AN: 152172 Hom.: 2583 Cov.: 32 AF XY: 0.171 AC XY: 12689 AN XY: 74406

Gnomad4 AFR AF: 0.248

Gnomad4 AMR AF: 0.131

Gnomad4 ASJ AF: 0.145

Gnomad4 EAS AF: 0.0544

Gnomad4 SAS AF: 0.150

Gnomad4 FIN AF: 0.134

Gnomad4 NFE AF: 0.160

Gnomad4 OTH AF: 0.175

Alfa AF: 0.175 Hom.: 291

Bravo AF: 0.177

Asia WGS AF: 0.119 AC: 414 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	1.4
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10264084; hg19: chr7-150592362;