rs1255372

Variant names:

• chr10-42496332-T-C
• rs1255372

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 0.701 in 152,014 control chromosomes in the GnomAD database, including 38,178 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 0.70 (38178 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.03
• Publications: 12 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.853 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: 0.701 AC: 106444 AN: 151896 Hom.: 38139 Cov.: 32

Gnomad AFR AF: 0.860

Gnomad AMI AF: 0.657

Gnomad AMR AF: 0.705

Gnomad ASJ AF: 0.668

Gnomad EAS AF: 0.638

Gnomad SAS AF: 0.602

Gnomad FIN AF: 0.686

Gnomad MID AF: 0.661

Gnomad NFE AF: 0.620

Gnomad OTH AF: 0.686

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

GnomAD4 genome AF: 0.701 AC: 106524 AN: 152014 Hom.: 38178 Cov.: 32 AF XY: 0.701 AC XY: 52101 AN XY: 74284

African (AFR) AF: 0.860 AC: 35696 AN: 41492

American (AMR) AF: 0.705 AC: 10777 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.668 AC: 2313 AN: 3462

East Asian (EAS) AF: 0.637 AC: 3285 AN: 5160

South Asian (SAS) AF: 0.599 AC: 2881 AN: 4808

European-Finnish (FIN) AF: 0.686 AC: 7235 AN: 10540

Middle Eastern (MID) AF: 0.663 AC: 195 AN: 294

European-Non Finnish (NFE) AF: 0.620 AC: 42108 AN: 67960

Other (OTH) AF: 0.681 AC: 1435 AN: 2108

Alfa AF: 0.646 Hom.: 121748

Bravo AF: 0.711

Asia WGS AF: 0.607 AC: 2115 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	3.1
DANN	Benign	0.53
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs1255372; hg19: chr10-42991780;