10-6361088-G-C

Position:

• chr10-6361088-G-C

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;