10-129293818-G-T

Variant names:

• chr10-129293818-G-T
• rs2246538

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 0.652 in 150,764 control chromosomes in the GnomAD database, including 32,999 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 0.65 (32999 hom., cov: 26)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0480
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.811 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: 0.652 AC: 98267 AN: 150644 Hom.: 32985 Cov.: 26

Gnomad AFR AF: 0.483

Gnomad AMI AF: 0.840

Gnomad AMR AF: 0.728

Gnomad ASJ AF: 0.708

Gnomad EAS AF: 0.593

Gnomad SAS AF: 0.832

Gnomad FIN AF: 0.694

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.718

Gnomad OTH AF: 0.657

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

GnomAD4 genome AF: 0.652 AC: 98316 AN: 150764 Hom.: 32999 Cov.: 26 AF XY: 0.654 AC XY: 48068 AN XY: 73542

African (AFR) AF: 0.482 AC: 19720 AN: 40916

American (AMR) AF: 0.729 AC: 10999 AN: 15094

Ashkenazi Jewish (ASJ) AF: 0.708 AC: 2451 AN: 3464

East Asian (EAS) AF: 0.592 AC: 3033 AN: 5120

South Asian (SAS) AF: 0.832 AC: 3931 AN: 4722

European-Finnish (FIN) AF: 0.694 AC: 7205 AN: 10380

Middle Eastern (MID) AF: 0.656 AC: 193 AN: 294

European-Non Finnish (NFE) AF: 0.718 AC: 48650 AN: 67782

Other (OTH) AF: 0.659 AC: 1375 AN: 2088

Alfa AF: 0.693 Hom.: 140860

Bravo AF: 0.645

Asia WGS AF: 0.702 AC: 2441 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.6
DANN	Benign	0.41
PhyloP100		-0.048

Splicing

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

Other links and lift over

dbSNP: rs2246538; hg19: chr10-131092082;