ENST00000741599.1:n.226+4913T>C

Variant names:

• chr5-155592305-T-C
• rs10515710
• ENST00000741599.1:n.226+4913T>C

Variant summary

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

The ENST00000741599.1(ENSG00000296753):​n.226+4913T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0424 in 152,324 control chromosomes in the GnomAD database, including 170 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 0.042 (170 hom., cov: 33)
• Consequence: ENSG00000296753 ENST00000741599.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0650
• Publications: 1 publications found

Genes affected

ENSG00000296753 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0787 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000741599.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000296753	ENST00000741599.1		n.226+4913T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0425 AC: 6466 AN: 152206 Hom.: 170 Cov.: 33

Gnomad AFR AF: 0.0218

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0298

Gnomad ASJ AF: 0.0901

Gnomad EAS AF: 0.000384

Gnomad SAS AF: 0.0857

Gnomad FIN AF: 0.0401

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0564

Gnomad OTH AF: 0.0445

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

GnomAD4 genome AF: 0.0424 AC: 6458 AN: 152324 Hom.: 170 Cov.: 33 AF XY: 0.0429 AC XY: 3196 AN XY: 74492

African (AFR) AF: 0.0217 AC: 902 AN: 41572

American (AMR) AF: 0.0297 AC: 455 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.0901 AC: 313 AN: 3472

East Asian (EAS) AF: 0.000385 AC: 2 AN: 5190

South Asian (SAS) AF: 0.0855 AC: 413 AN: 4828

European-Finnish (FIN) AF: 0.0401 AC: 426 AN: 10614

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.0564 AC: 3835 AN: 68024

Other (OTH) AF: 0.0431 AC: 91 AN: 2112

Alfa AF: 0.0548 Hom.: 139

Bravo AF: 0.0383

Asia WGS AF: 0.0300 AC: 104 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.9
DANN	Benign	0.45
PhyloP100		0.065

Splicing

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

Other links and lift over

dbSNP: rs10515710; hg19: chr5-154971865; COSMIC: COSV60218930;