rs10254572

Variant names:

• chr7-12408856-C-T
• rs10254572

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 0.182 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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.352 AC: 14603 AN: 41470

American (AMR) AF: 0.0992 AC: 1517 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0824 AC: 286 AN: 3470

East Asian (EAS) AF: 0.133 AC: 690 AN: 5176

South Asian (SAS) AF: 0.133 AC: 638 AN: 4808

European-Finnish (FIN) AF: 0.120 AC: 1274 AN: 10592

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.121 AC: 8249 AN: 68004

Other (OTH) AF: 0.142 AC: 300 AN: 2112

Alfa AF: 0.137 Hom.: 925

Bravo AF: 0.188

Asia WGS AF: 0.134 AC: 464 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	8.3
DANN	Benign	0.46
PhyloP100		0.70

Splicing

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

Other links and lift over

dbSNP: rs10254572; hg19: chr7-12448482;