10-117226885-G-A

Position:

• chr10-117226885-G-A

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 0.199 in 152,128 control chromosomes in the GnomAD database, including 3,658 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 0.20 (3658 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.912

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.541 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: 0.199 AC: 30269 AN: 152010 Hom.: 3649 Cov.: 32

Gnomad AFR AF: 0.119

Gnomad AMI AF: 0.414

Gnomad AMR AF: 0.154

Gnomad ASJ AF: 0.159

Gnomad EAS AF: 0.558

Gnomad SAS AF: 0.332

Gnomad FIN AF: 0.174

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.225

Gnomad OTH AF: 0.183

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

GnomAD4 genome AF: 0.199 AC: 30298 AN: 152128 Hom.: 3658 Cov.: 32 AF XY: 0.199 AC XY: 14823 AN XY: 74364

Gnomad4 AFR AF: 0.119

Gnomad4 AMR AF: 0.155

Gnomad4 ASJ AF: 0.159

Gnomad4 EAS AF: 0.558

Gnomad4 SAS AF: 0.330

Gnomad4 FIN AF: 0.174

Gnomad4 NFE AF: 0.225

Gnomad4 OTH AF: 0.192

Alfa AF: 0.209 Hom.: 3453

Bravo AF: 0.194

Asia WGS AF: 0.437 AC: 1518 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	0.96
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs363371; hg19: chr10-118986396;