5-155434249-T-C

Variant names:

• chr5-155434249-T-C
• rs10476823
• ENST00000758995.1:n.298+16958T>C

Variant summary

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

The ENST00000758995.1(ENSG00000298918):​n.298+16958T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.181 in 152,150 control chromosomes in the GnomAD database, including 2,850 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 0.18 (2850 hom., cov: 32)
• Consequence: ENSG00000298918 ENST00000758995.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00300
• Publications: 1 publications found

Genes affected

ENSG00000298918 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.28 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000758995.1. 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
	ENSG00000298918	ENST00000758995.1		n.298+16958T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.181 AC: 27519 AN: 152032 Hom.: 2844 Cov.: 32

Gnomad AFR AF: 0.285

Gnomad AMI AF: 0.333

Gnomad AMR AF: 0.136

Gnomad ASJ AF: 0.152

Gnomad EAS AF: 0.0398

Gnomad SAS AF: 0.171

Gnomad FIN AF: 0.105

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.151

Gnomad OTH AF: 0.178

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

GnomAD4 genome AF: 0.181 AC: 27543 AN: 152150 Hom.: 2850 Cov.: 32 AF XY: 0.177 AC XY: 13139 AN XY: 74384

African (AFR) AF: 0.284 AC: 11800 AN: 41494

American (AMR) AF: 0.135 AC: 2068 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.152 AC: 528 AN: 3468

East Asian (EAS) AF: 0.0398 AC: 206 AN: 5170

South Asian (SAS) AF: 0.171 AC: 827 AN: 4830

European-Finnish (FIN) AF: 0.105 AC: 1114 AN: 10602

Middle Eastern (MID) AF: 0.218 AC: 64 AN: 294

European-Non Finnish (NFE) AF: 0.151 AC: 10255 AN: 67988

Other (OTH) AF: 0.179 AC: 378 AN: 2114

Alfa AF: 0.137 Hom.: 839

Bravo AF: 0.187

Asia WGS AF: 0.120 AC: 418 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	8.6
DANN	Benign	0.60
PhyloP100		0.0030

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10476823;

hg19: chr5-154813809;

COSMIC: COSV60217995;