chr10-19811890-T-C

Position:

• chr10-19811890-T-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 0.0899 in 152,312 control chromosomes in the GnomAD database, including 787 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 0.090 (787 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.342

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 (AFR) allele frequency at 95% confidence interval = 0.152 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: 0.0898 AC: 13665 AN: 152194 Hom.: 783 Cov.: 33

Gnomad AFR AF: 0.155

Gnomad AMI AF: 0.0713

Gnomad AMR AF: 0.0595

Gnomad ASJ AF: 0.0591

Gnomad EAS AF: 0.0581

Gnomad SAS AF: 0.101

Gnomad FIN AF: 0.0362

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.0686

Gnomad OTH AF: 0.0831

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

GnomAD4 genome AF: 0.0899 AC: 13700 AN: 152312 Hom.: 787 Cov.: 33 AF XY: 0.0885 AC XY: 6593 AN XY: 74486

Gnomad4 AFR AF: 0.155

Gnomad4 AMR AF: 0.0595

Gnomad4 ASJ AF: 0.0591

Gnomad4 EAS AF: 0.0580

Gnomad4 SAS AF: 0.101

Gnomad4 FIN AF: 0.0362

Gnomad4 NFE AF: 0.0686

Gnomad4 OTH AF: 0.0888

Alfa AF: 0.0750 Hom.: 381

Bravo AF: 0.0931

Asia WGS AF: 0.101 AC: 354 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	2.7
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11011581; hg19: chr10-20100819;