chr10-99531836-T-C

Position:

• chr10-99531836-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 0.553 in 152,068 control chromosomes in the GnomAD database, including 23,519 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 (23519 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.47

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.61 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: 0.553 AC: 83995 AN: 151950 Hom.: 23488 Cov.: 33

Gnomad AFR AF: 0.616

Gnomad AMI AF: 0.483

Gnomad AMR AF: 0.578

Gnomad ASJ AF: 0.463

Gnomad EAS AF: 0.553

Gnomad SAS AF: 0.627

Gnomad FIN AF: 0.514

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.516

Gnomad OTH AF: 0.522

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

GnomAD4 genome AF: 0.553 AC: 84078 AN: 152068 Hom.: 23519 Cov.: 33 AF XY: 0.554 AC XY: 41181 AN XY: 74340

Gnomad4 AFR AF: 0.616

Gnomad4 AMR AF: 0.579

Gnomad4 ASJ AF: 0.463

Gnomad4 EAS AF: 0.553

Gnomad4 SAS AF: 0.626

Gnomad4 FIN AF: 0.514

Gnomad4 NFE AF: 0.516

Gnomad4 OTH AF: 0.518

Alfa AF: 0.520 Hom.: 44928

Bravo AF: 0.558

Asia WGS AF: 0.605 AC: 2105 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	6.2
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11190140; hg19: chr10-101291593;