10-4951623-C-T

Variant names:

• chr10-4951623-C-T
• rs11252845
• ENST00000806558.1:n.265-1174C>T

Variant summary

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

The ENST00000806558.1(ENSG00000304836):​n.265-1174C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0411 in 152,250 control chromosomes in the GnomAD database, including 208 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 0.041 (208 hom., cov: 33)
• Consequence: ENSG00000304836 ENST00000806558.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.899
• Publications: 4 publications found

Genes affected

ENSG00000304836 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0579 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
ENSG00000304836	ENST00000806558.1	n.265-1174C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.0412 AC: 6263 AN: 152132 Hom.: 208 Cov.: 33

Gnomad AFR AF: 0.0114

Gnomad AMI AF: 0.0482

Gnomad AMR AF: 0.0481

Gnomad ASJ AF: 0.161

Gnomad EAS AF: 0.000386

Gnomad SAS AF: 0.0184

Gnomad FIN AF: 0.0161

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0595

Gnomad OTH AF: 0.0593

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

GnomAD4 genome AF: 0.0411 AC: 6258 AN: 152250 Hom.: 208 Cov.: 33 AF XY: 0.0392 AC XY: 2918 AN XY: 74440

African (AFR) AF: 0.0114 AC: 473 AN: 41556

American (AMR) AF: 0.0480 AC: 734 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.161 AC: 560 AN: 3472

East Asian (EAS) AF: 0.000387 AC: 2 AN: 5168

South Asian (SAS) AF: 0.0183 AC: 88 AN: 4820

European-Finnish (FIN) AF: 0.0161 AC: 171 AN: 10608

Middle Eastern (MID) AF: 0.0612 AC: 18 AN: 294

European-Non Finnish (NFE) AF: 0.0595 AC: 4044 AN: 68022

Other (OTH) AF: 0.0587 AC: 124 AN: 2114

Alfa AF: 0.0542 Hom.: 141

Bravo AF: 0.0421

Asia WGS AF: 0.0110 AC: 37 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.69
DANN	Benign	0.24
PhyloP100		-0.90
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs11252845; hg19: chr10-4993815;