chr12-10800458-T-C

Position:

• chr12-10800458-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 0.746 in 152,056 control chromosomes in the GnomAD database, including 42,517 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 0.75 (42517 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0720

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.769 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.10800458T>C		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.746 AC: 113313 AN: 151938 Hom.: 42482 Cov.: 32

Gnomad AFR AF: 0.683

Gnomad AMI AF: 0.923

Gnomad AMR AF: 0.729

Gnomad ASJ AF: 0.831

Gnomad EAS AF: 0.723

Gnomad SAS AF: 0.686

Gnomad FIN AF: 0.822

Gnomad MID AF: 0.816

Gnomad NFE AF: 0.774

Gnomad OTH AF: 0.755

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

GnomAD4 genome AF: 0.746 AC: 113393 AN: 152056 Hom.: 42517 Cov.: 32 AF XY: 0.745 AC XY: 55384 AN XY: 74326

Gnomad4 AFR AF: 0.684

Gnomad4 AMR AF: 0.728

Gnomad4 ASJ AF: 0.831

Gnomad4 EAS AF: 0.723

Gnomad4 SAS AF: 0.686

Gnomad4 FIN AF: 0.822

Gnomad4 NFE AF: 0.774

Gnomad4 OTH AF: 0.754

Alfa AF: 0.773 Hom.: 75984

Bravo AF: 0.735

Asia WGS AF: 0.705 AC: 2451 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.7
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2588350; hg19: chr12-10953057;