rs10254572

Variant names:

• chr7-12408856-C-T
• rs10254572

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 0.182 in 152,128 control chromosomes in the GnomAD database, including 3,387 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 (3387 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.701

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.347 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: 0.182 AC: 27643 AN: 152010 Hom.: 3373 Cov.: 32

Gnomad AFR AF: 0.352

Gnomad AMI AF: 0.103

Gnomad AMR AF: 0.0994

Gnomad ASJ AF: 0.0824

Gnomad EAS AF: 0.133

Gnomad SAS AF: 0.134

Gnomad FIN AF: 0.120

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.121

Gnomad OTH AF: 0.143

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

GnomAD4 genome AF: 0.182 AC: 27687 AN: 152128 Hom.: 3387 Cov.: 32 AF XY: 0.181 AC XY: 13453 AN XY: 74360

Gnomad4 AFR AF: 0.352

Gnomad4 AMR AF: 0.0992

Gnomad4 ASJ AF: 0.0824

Gnomad4 EAS AF: 0.133

Gnomad4 SAS AF: 0.133

Gnomad4 FIN AF: 0.120

Gnomad4 NFE AF: 0.121

Gnomad4 OTH AF: 0.142

Alfa AF: 0.136 Hom.: 806

Bravo AF: 0.188

Asia WGS AF: 0.134 AC: 464 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	8.3
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10254572; hg19: chr7-12448482;