chr10-120355871-C-T

Variant names:

• chr10-120355871-C-T
• rs2901228

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 0.763 in 152,156 control chromosomes in the GnomAD database, including 44,679 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 0.76 (44679 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.557

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 (SAS) allele frequency at 95% confidence interval = 0.825 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: 0.763 AC: 116060 AN: 152040 Hom.: 44630 Cov.: 32

Gnomad AFR AF: 0.814

Gnomad AMI AF: 0.860

Gnomad AMR AF: 0.618

Gnomad ASJ AF: 0.715

Gnomad EAS AF: 0.809

Gnomad SAS AF: 0.846

Gnomad FIN AF: 0.785

Gnomad MID AF: 0.756

Gnomad NFE AF: 0.754

Gnomad OTH AF: 0.748

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

GnomAD4 genome AF: 0.763 AC: 116155 AN: 152156 Hom.: 44679 Cov.: 32 AF XY: 0.764 AC XY: 56859 AN XY: 74392

Gnomad4 AFR AF: 0.814

Gnomad4 AMR AF: 0.618

Gnomad4 ASJ AF: 0.715

Gnomad4 EAS AF: 0.809

Gnomad4 SAS AF: 0.846

Gnomad4 FIN AF: 0.785

Gnomad4 NFE AF: 0.754

Gnomad4 OTH AF: 0.751

Alfa AF: 0.758 Hom.: 8875

Bravo AF: 0.750

Asia WGS AF: 0.817 AC: 2844 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	3.6
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2901228; hg19: chr10-122115383;