10-129228428-T-G

Variant names:

• chr10-129228428-T-G
• rs1861860

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 0.176 in 152,220 control chromosomes in the GnomAD database, including 2,510 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 0.18 (2510 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.48

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.287 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: 0.176 AC: 26796 AN: 152100 Hom.: 2511 Cov.: 33

Gnomad AFR AF: 0.127

Gnomad AMI AF: 0.129

Gnomad AMR AF: 0.196

Gnomad ASJ AF: 0.171

Gnomad EAS AF: 0.219

Gnomad SAS AF: 0.300

Gnomad FIN AF: 0.215

Gnomad MID AF: 0.185

Gnomad NFE AF: 0.185

Gnomad OTH AF: 0.170

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

GnomAD4 genome AF: 0.176 AC: 26803 AN: 152220 Hom.: 2510 Cov.: 33 AF XY: 0.179 AC XY: 13341 AN XY: 74428

Gnomad4 AFR AF: 0.127

Gnomad4 AMR AF: 0.196

Gnomad4 ASJ AF: 0.171

Gnomad4 EAS AF: 0.219

Gnomad4 SAS AF: 0.300

Gnomad4 FIN AF: 0.215

Gnomad4 NFE AF: 0.185

Gnomad4 OTH AF: 0.172

Alfa AF: 0.182 Hom.: 922

Bravo AF: 0.171

Asia WGS AF: 0.248 AC: 862 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.10
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1861860; hg19: chr10-131026692;