rs10491146

Variant names:

• chr17-50628796-C-G
• rs10491146
• ENST00000502435.1:n.202-1456G>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000502435.1(ENSG00000251239):​n.202-1456G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0187 in 152,296 control chromosomes in the GnomAD database, including 54 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 0.019 (54 hom., cov: 32)
• Consequence: ENSG00000251239 ENST00000502435.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.219

Genes affected

ENSG00000251239 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0187 (2855/152296) while in subpopulation NFE AF = 0.03 (2040/68014). AF 95% confidence interval is 0.0289. There are 54 homozygotes in GnomAd4. There are 1357 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position FAILED quality control check.
• BS2: High Homozygotes in GnomAd4 at 54 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101927253	XR_243718.2	n.202-1456G>C		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000251239	ENST00000502435.1	n.202-1456G>C		intron_variant	Intron 1 of 1	2

Frequencies

GnomAD3 genomes AF: 0.0188 AC: 2855 AN: 152178 Hom.: 54 Cov.: 32

Gnomad AFR AF: 0.00444

Gnomad AMI AF: 0.0121

Gnomad AMR AF: 0.0100

Gnomad ASJ AF: 0.00663

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.00289

Gnomad FIN AF: 0.0378

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0300

Gnomad OTH AF: 0.0105

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

GnomAD4 genome AF: 0.0187 AC: 2855 AN: 152296 Hom.: 54 Cov.: 32 AF XY: 0.0182 AC XY: 1357 AN XY: 74472

Gnomad4 AFR AF: 0.00440 AC: 0.00440412 AN: 0.00440412

Gnomad4 AMR AF: 0.00999 AC: 0.00999477 AN: 0.00999477

Gnomad4 ASJ AF: 0.00663 AC: 0.00662824 AN: 0.00662824

Gnomad4 EAS AF: 0.000193 AC: 0.00019305 AN: 0.00019305

Gnomad4 SAS AF: 0.00290 AC: 0.00289735 AN: 0.00289735

Gnomad4 FIN AF: 0.0378 AC: 0.0377661 AN: 0.0377661

Gnomad4 NFE AF: 0.0300 AC: 0.0299938 AN: 0.0299938

Gnomad4 OTH AF: 0.0104 AC: 0.010397 AN: 0.010397

Alfa AF: 0.0229 Hom.: 8

Bravo AF: 0.0163

Asia WGS AF: 0.00231 AC: 8 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	0.52
DANN	Benign	0.57
Mutation Taster		=100/0	polymorphism

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10491146; hg19: chr17-48706157;