10-89141369-C-T

Variant names:

• chr10-89141369-C-T
• rs2251050

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 0.37 in 151,908 control chromosomes in the GnomAD database, including 10,875 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 0.37 (10875 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.978
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.669 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: 0.370 AC: 56112 AN: 151790 Hom.: 10868 Cov.: 32

Gnomad AFR AF: 0.295

Gnomad AMI AF: 0.395

Gnomad AMR AF: 0.373

Gnomad ASJ AF: 0.326

Gnomad EAS AF: 0.688

Gnomad SAS AF: 0.415

Gnomad FIN AF: 0.450

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.377

Gnomad OTH AF: 0.369

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

GnomAD4 genome AF: 0.370 AC: 56147 AN: 151908 Hom.: 10875 Cov.: 32 AF XY: 0.376 AC XY: 27931 AN XY: 74248

African (AFR) AF: 0.295 AC: 12219 AN: 41446

American (AMR) AF: 0.373 AC: 5689 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.326 AC: 1131 AN: 3470

East Asian (EAS) AF: 0.688 AC: 3554 AN: 5164

South Asian (SAS) AF: 0.416 AC: 2004 AN: 4816

European-Finnish (FIN) AF: 0.450 AC: 4727 AN: 10514

Middle Eastern (MID) AF: 0.333 AC: 98 AN: 294

European-Non Finnish (NFE) AF: 0.377 AC: 25587 AN: 67942

Other (OTH) AF: 0.370 AC: 779 AN: 2106

Alfa AF: 0.371 Hom.: 5541

Bravo AF: 0.365

Asia WGS AF: 0.527 AC: 1833 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.2
DANN	Benign	0.44
PhyloP100		-0.98

Splicing

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

Other links and lift over

dbSNP: rs2251050; hg19: chr10-90901126;