10-130783070-C-T

Variant names:

• chr10-130783070-C-T
• rs1911999
• ENST00000754524.1:n.509+198G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000754524.1(ENSG00000298296):​n.509+198G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.505 in 152,036 control chromosomes in the GnomAD database, including 23,525 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 0.50 (23525 hom., cov: 33)
• Consequence: ENSG00000298296 ENST00000754524.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.90
• Publications: 3 publications found

Genes affected

ENSG00000298296 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.713 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000298296	ENST00000754524.1	n.509+198G>A		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.505 AC: 76752 AN: 151918 Hom.: 23531 Cov.: 33

Gnomad AFR AF: 0.131

Gnomad AMI AF: 0.781

Gnomad AMR AF: 0.612

Gnomad ASJ AF: 0.655

Gnomad EAS AF: 0.732

Gnomad SAS AF: 0.536

Gnomad FIN AF: 0.654

Gnomad MID AF: 0.602

Gnomad NFE AF: 0.654

Gnomad OTH AF: 0.525

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

GnomAD4 genome AF: 0.505 AC: 76735 AN: 152036 Hom.: 23525 Cov.: 33 AF XY: 0.509 AC XY: 37813 AN XY: 74290

African (AFR) AF: 0.130 AC: 5405 AN: 41494

American (AMR) AF: 0.612 AC: 9355 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.655 AC: 2273 AN: 3470

East Asian (EAS) AF: 0.732 AC: 3762 AN: 5138

South Asian (SAS) AF: 0.537 AC: 2585 AN: 4818

European-Finnish (FIN) AF: 0.654 AC: 6898 AN: 10542

Middle Eastern (MID) AF: 0.603 AC: 176 AN: 292

European-Non Finnish (NFE) AF: 0.654 AC: 44475 AN: 67978

Other (OTH) AF: 0.519 AC: 1098 AN: 2114

Alfa AF: 0.599 Hom.: 84943

Bravo AF: 0.486

Asia WGS AF: 0.547 AC: 1901 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	0.16
DANN	Benign	0.57
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs1911999; hg19: chr10-132581334;