10-18131455-G-A

Position:

• chr10-18131455-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 0.243 in 152,010 control chromosomes in the GnomAD database, including 4,796 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 0.24 (4796 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.328

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 (EAS) allele frequency at 95% confidence interval = 0.34 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.243 AC: 36876 AN: 151890 Hom.: 4774 Cov.: 33

Gnomad AFR AF: 0.219

Gnomad AMI AF: 0.200

Gnomad AMR AF: 0.271

Gnomad ASJ AF: 0.192

Gnomad EAS AF: 0.353

Gnomad SAS AF: 0.215

Gnomad FIN AF: 0.402

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.223

Gnomad OTH AF: 0.245

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

GnomAD4 genome AF: 0.243 AC: 36942 AN: 152010 Hom.: 4796 Cov.: 33 AF XY: 0.252 AC XY: 18719 AN XY: 74290

Gnomad4 AFR AF: 0.219

Gnomad4 AMR AF: 0.271

Gnomad4 ASJ AF: 0.192

Gnomad4 EAS AF: 0.353

Gnomad4 SAS AF: 0.216

Gnomad4 FIN AF: 0.402

Gnomad4 NFE AF: 0.223

Gnomad4 OTH AF: 0.252

Alfa AF: 0.228 Hom.: 6918

Bravo AF: 0.235

Asia WGS AF: 0.252 AC: 875 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	3.0
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11596974; hg19: chr10-18420384;