10-6361088-G-C

Variant names:

• chr10-6361088-G-C
• rs2146900

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 0.821 in 151,946 control chromosomes in the GnomAD database, including 51,347 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 0.82 (51347 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.790

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.953 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: 0.821 AC: 124680 AN: 151828 Hom.: 51302 Cov.: 29

Gnomad AFR AF: 0.774

Gnomad AMI AF: 0.851

Gnomad AMR AF: 0.881

Gnomad ASJ AF: 0.819

Gnomad EAS AF: 0.976

Gnomad SAS AF: 0.857

Gnomad FIN AF: 0.823

Gnomad MID AF: 0.801

Gnomad NFE AF: 0.821

Gnomad OTH AF: 0.824

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

GnomAD4 genome AF: 0.821 AC: 124780 AN: 151946 Hom.: 51347 Cov.: 29 AF XY: 0.824 AC XY: 61207 AN XY: 74248

Gnomad4 AFR AF: 0.774

Gnomad4 AMR AF: 0.882

Gnomad4 ASJ AF: 0.819

Gnomad4 EAS AF: 0.975

Gnomad4 SAS AF: 0.858

Gnomad4 FIN AF: 0.823

Gnomad4 NFE AF: 0.821

Gnomad4 OTH AF: 0.821

Alfa AF: 0.771 Hom.: 2312

Bravo AF: 0.823

Asia WGS AF: 0.908 AC: 3158 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.0
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2146900; hg19: chr10-6403050;