19-10131268-C-T

Position:

• chr19-10131268-C-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 0.607 in 151,728 control chromosomes in the GnomAD database, including 28,405 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 0.61 (28405 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.763

Genes affected

(HGNC:):

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 = 0.705 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.10131268C>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.607 AC: 92023 AN: 151610 Hom.: 28369 Cov.: 31

Gnomad AFR AF: 0.666

Gnomad AMI AF: 0.515

Gnomad AMR AF: 0.698

Gnomad ASJ AF: 0.550

Gnomad EAS AF: 0.724

Gnomad SAS AF: 0.680

Gnomad FIN AF: 0.534

Gnomad MID AF: 0.560

Gnomad NFE AF: 0.552

Gnomad OTH AF: 0.626

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

GnomAD4 genome AF: 0.607 AC: 92118 AN: 151728 Hom.: 28405 Cov.: 31 AF XY: 0.611 AC XY: 45312 AN XY: 74156

Gnomad4 AFR AF: 0.666

Gnomad4 AMR AF: 0.698

Gnomad4 ASJ AF: 0.550

Gnomad4 EAS AF: 0.724

Gnomad4 SAS AF: 0.680

Gnomad4 FIN AF: 0.534

Gnomad4 NFE AF: 0.552

Gnomad4 OTH AF: 0.622

Alfa AF: 0.578 Hom.: 25518

Bravo AF: 0.626

Asia WGS AF: 0.681 AC: 2370 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.20
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4804122; hg19: chr19-10241944;