10-128571226-T-C

Variant names:

• chr10-128571226-T-C
• rs749141

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 0.133 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
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• 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

African (AFR) AF: 0.230 AC: 9552 AN: 41512

American (AMR) AF: 0.0753 AC: 1152 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0809 AC: 281 AN: 3472

East Asian (EAS) AF: 0.431 AC: 2220 AN: 5152

South Asian (SAS) AF: 0.213 AC: 1025 AN: 4820

European-Finnish (FIN) AF: 0.0865 AC: 917 AN: 10602

Middle Eastern (MID) AF: 0.0884 AC: 26 AN: 294

European-Non Finnish (NFE) AF: 0.0691 AC: 4698 AN: 68004

Other (OTH) AF: 0.117 AC: 247 AN: 2116

Alfa AF: 0.105 Hom.: 141

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
PhyloP100		-2.4

Splicing

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

Other links and lift over

dbSNP: rs749141; hg19: chr10-130369490;