10-36819981-G-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 0.396 in 151,908 control chromosomes in the GnomAD database, including 12,453 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 0.40 (12453 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.123

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.72 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: 0.396 AC: 60142 AN: 151786 Hom.: 12443 Cov.: 34

Gnomad AFR AF: 0.361

Gnomad AMI AF: 0.307

Gnomad AMR AF: 0.445

Gnomad ASJ AF: 0.343

Gnomad EAS AF: 0.739

Gnomad SAS AF: 0.626

Gnomad FIN AF: 0.394

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.368

Gnomad OTH AF: 0.388

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

GnomAD4 genome AF: 0.396 AC: 60170 AN: 151908 Hom.: 12453 Cov.: 34 AF XY: 0.404 AC XY: 30001 AN XY: 74238

Gnomad4 AFR AF: 0.360

Gnomad4 AMR AF: 0.445

Gnomad4 ASJ AF: 0.343

Gnomad4 EAS AF: 0.740

Gnomad4 SAS AF: 0.626

Gnomad4 FIN AF: 0.394

Gnomad4 NFE AF: 0.368

Gnomad4 OTH AF: 0.390

Alfa AF: 0.219 Hom.: 444

Bravo AF: 0.396

Asia WGS AF: 0.665 AC: 2310 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	2.1
Dann	Benign	0.27

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11817755; hg19: chr10-37108909;