10-36822586-C-T

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 0.488 in 152,082 control chromosomes in the GnomAD database, including 18,548 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 0.49 (18548 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.164

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.721 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: 0.488 AC: 74213 AN: 151962 Hom.: 18530 Cov.: 33

Gnomad AFR AF: 0.504

Gnomad AMI AF: 0.351

Gnomad AMR AF: 0.518

Gnomad ASJ AF: 0.455

Gnomad EAS AF: 0.740

Gnomad SAS AF: 0.654

Gnomad FIN AF: 0.453

Gnomad MID AF: 0.562

Gnomad NFE AF: 0.450

Gnomad OTH AF: 0.480

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

GnomAD4 genome AF: 0.488 AC: 74258 AN: 152082 Hom.: 18548 Cov.: 33 AF XY: 0.493 AC XY: 36628 AN XY: 74330

Gnomad4 AFR AF: 0.504

Gnomad4 AMR AF: 0.518

Gnomad4 ASJ AF: 0.455

Gnomad4 EAS AF: 0.740

Gnomad4 SAS AF: 0.654

Gnomad4 FIN AF: 0.453

Gnomad4 NFE AF: 0.450

Gnomad4 OTH AF: 0.481

Alfa AF: 0.458 Hom.: 3912

Bravo AF: 0.493

Asia WGS AF: 0.690 AC: 2396 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	3.2
Dann	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3867222; hg19: chr10-37111514;