rs62494762

Variant names:

• chr8-5516018-T-C
• rs62494762
• ENST00000804953.1:n.130+5779T>C

Variant summary

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

The ENST00000804953.1(ENSG00000304614):​n.130+5779T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.202 in 152,018 control chromosomes in the GnomAD database, including 3,222 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 0.20 (3222 hom., cov: 32)
• Consequence: ENSG00000304614 ENST00000804953.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.88
• Publications: 0 publications found

Genes affected

ENSG00000304614 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.247 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000804953.1. 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
	ENSG00000304614	ENST00000804953.1		n.130+5779T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.202 AC: 30726 AN: 151898 Hom.: 3222 Cov.: 32

Gnomad AFR AF: 0.154

Gnomad AMI AF: 0.324

Gnomad AMR AF: 0.200

Gnomad ASJ AF: 0.247

Gnomad EAS AF: 0.259

Gnomad SAS AF: 0.237

Gnomad FIN AF: 0.129

Gnomad MID AF: 0.296

Gnomad NFE AF: 0.232

Gnomad OTH AF: 0.223

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

GnomAD4 genome AF: 0.202 AC: 30735 AN: 152018 Hom.: 3222 Cov.: 32 AF XY: 0.199 AC XY: 14772 AN XY: 74312

African (AFR) AF: 0.154 AC: 6395 AN: 41496

American (AMR) AF: 0.200 AC: 3055 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.247 AC: 858 AN: 3468

East Asian (EAS) AF: 0.259 AC: 1327 AN: 5124

South Asian (SAS) AF: 0.236 AC: 1134 AN: 4810

European-Finnish (FIN) AF: 0.129 AC: 1365 AN: 10602

Middle Eastern (MID) AF: 0.295 AC: 86 AN: 292

European-Non Finnish (NFE) AF: 0.232 AC: 15752 AN: 67930

Other (OTH) AF: 0.221 AC: 468 AN: 2114

Alfa AF: 0.222 Hom.: 7105

Bravo AF: 0.206

Asia WGS AF: 0.234 AC: 812 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.12
DANN	Benign	0.20
PhyloP100		-1.9

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: rs62494762;

hg19: chr8-5373540;