rs10454657

Variant names:

• chr13-75017686-C-T
• rs10454657
• ENST00000807127.1:n.110+4827G>A

Variant summary

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

The ENST00000807127.1(ENSG00000304923):​n.110+4827G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.479 in 151,736 control chromosomes in the GnomAD database, including 19,212 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 0.48 (19212 hom., cov: 31)
• Consequence: ENSG00000304923 ENST00000807127.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.45
• Publications: 4 publications found

Genes affected

ENSG00000304923 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.578 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107984620	XR_001749917.1	n.257+4827G>A		intron_variant	Intron 3 of 3
LOC107984620	XR_001749918.1	n.208+4827G>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000304923	ENST00000807127.1	n.110+4827G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.480 AC: 72743 AN: 151618 Hom.: 19216 Cov.: 31

Gnomad AFR AF: 0.242

Gnomad AMI AF: 0.617

Gnomad AMR AF: 0.547

Gnomad ASJ AF: 0.553

Gnomad EAS AF: 0.563

Gnomad SAS AF: 0.430

Gnomad FIN AF: 0.587

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.583

Gnomad OTH AF: 0.511

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

GnomAD4 genome AF: 0.479 AC: 72743 AN: 151736 Hom.: 19212 Cov.: 31 AF XY: 0.479 AC XY: 35470 AN XY: 74114

African (AFR) AF: 0.242 AC: 10008 AN: 41338

American (AMR) AF: 0.547 AC: 8331 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.553 AC: 1914 AN: 3464

East Asian (EAS) AF: 0.562 AC: 2892 AN: 5148

South Asian (SAS) AF: 0.430 AC: 2070 AN: 4812

European-Finnish (FIN) AF: 0.587 AC: 6160 AN: 10498

Middle Eastern (MID) AF: 0.517 AC: 151 AN: 292

European-Non Finnish (NFE) AF: 0.583 AC: 39589 AN: 67940

Other (OTH) AF: 0.508 AC: 1065 AN: 2098

Alfa AF: 0.541 Hom.: 77236

Bravo AF: 0.470

Asia WGS AF: 0.502 AC: 1741 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.076
DANN	Benign	0.61
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs10454657; hg19: chr13-75591823;