XR_001749917.1:n.257+4827G>A

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 XR_001749917.1(LOC107984620):​n.257+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: LOC107984620 XR_001749917.1 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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000807127.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000304923	ENST00000807127.1		n.110+4827G>A		intron	N/A

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 v4.9

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;