10-36822586-C-T

Variant names:

• chr10-36822586-C-T
• rs3867222

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;