10-36819307-T-A

Position:

• chr10-36819307-T-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 0.547 in 152,002 control chromosomes in the GnomAD database, including 23,053 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 0.55 (23053 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.700

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.764 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.547 AC: 83068 AN: 151884 Hom.: 23030 Cov.: 33

Gnomad AFR AF: 0.541

Gnomad AMI AF: 0.416

Gnomad AMR AF: 0.559

Gnomad ASJ AF: 0.525

Gnomad EAS AF: 0.783

Gnomad SAS AF: 0.722

Gnomad FIN AF: 0.523

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.524

Gnomad OTH AF: 0.532

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

GnomAD4 genome AF: 0.547 AC: 83123 AN: 152002 Hom.: 23053 Cov.: 33 AF XY: 0.551 AC XY: 40920 AN XY: 74282

Gnomad4 AFR AF: 0.541

Gnomad4 AMR AF: 0.559

Gnomad4 ASJ AF: 0.525

Gnomad4 EAS AF: 0.784

Gnomad4 SAS AF: 0.722

Gnomad4 FIN AF: 0.523

Gnomad4 NFE AF: 0.524

Gnomad4 OTH AF: 0.534

Alfa AF: 0.523 Hom.: 2497

Bravo AF: 0.549

Asia WGS AF: 0.737 AC: 2550 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.4
DANN	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2463226; hg19: chr10-37108235;