10-128571226-T-C

Variant names:

• chr10-128571226-T-C
• rs749141

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 0.133 in 152,186 control chromosomes in the GnomAD database, including 1,984 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 0.13 (1984 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.42

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.416 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: 0.133 AC: 20179 AN: 152068 Hom.: 1977 Cov.: 33

Gnomad AFR AF: 0.230

Gnomad AMI AF: 0.114

Gnomad AMR AF: 0.0753

Gnomad ASJ AF: 0.0809

Gnomad EAS AF: 0.432

Gnomad SAS AF: 0.213

Gnomad FIN AF: 0.0865

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.0691

Gnomad OTH AF: 0.112

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

GnomAD4 genome AF: 0.133 AC: 20222 AN: 152186 Hom.: 1984 Cov.: 33 AF XY: 0.134 AC XY: 9967 AN XY: 74402

Gnomad4 AFR AF: 0.230

Gnomad4 AMR AF: 0.0753

Gnomad4 ASJ AF: 0.0809

Gnomad4 EAS AF: 0.431

Gnomad4 SAS AF: 0.213

Gnomad4 FIN AF: 0.0865

Gnomad4 NFE AF: 0.0691

Gnomad4 OTH AF: 0.117

Alfa AF: 0.101 Hom.: 122

Bravo AF: 0.136

Asia WGS AF: 0.304 AC: 1055 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.37
DANN	Benign	0.18

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs749141; hg19: chr10-130369490;