10-36818338-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 0.133 in 152,238 control chromosomes in the GnomAD database, including 1,551 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 0.13 (1551 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02

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 (AMR) allele frequency at 95% confidence interval = 0.193 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: 0.133 AC: 20283 AN: 152120 Hom.: 1550 Cov.: 33

Gnomad AFR AF: 0.0875

Gnomad AMI AF: 0.231

Gnomad AMR AF: 0.199

Gnomad ASJ AF: 0.144

Gnomad EAS AF: 0.0854

Gnomad SAS AF: 0.0799

Gnomad FIN AF: 0.101

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.157

Gnomad OTH AF: 0.155

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

GnomAD4 genome AF: 0.133 AC: 20294 AN: 152238 Hom.: 1551 Cov.: 33 AF XY: 0.132 AC XY: 9846 AN XY: 74428

Gnomad4 AFR AF: 0.0874

Gnomad4 AMR AF: 0.199

Gnomad4 ASJ AF: 0.144

Gnomad4 EAS AF: 0.0852

Gnomad4 SAS AF: 0.0812

Gnomad4 FIN AF: 0.101

Gnomad4 NFE AF: 0.157

Gnomad4 OTH AF: 0.154

Alfa AF: 0.0455 Hom.: 62

Bravo AF: 0.141

Asia WGS AF: 0.0710 AC: 248 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	0.45
Dann	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2695081; hg19: chr10-37107266;