rs62094879

Variant names:

• chr18-57829073-C-T
• rs62094879
• ENST00000791946.1:n.261-4038C>T

Variant summary

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

The ENST00000791946.1(ENSG00000303117):​n.261-4038C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.143 in 151,850 control chromosomes in the GnomAD database, including 1,840 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 0.14 (1840 hom., cov: 29)
• Consequence: ENSG00000303117 ENST00000791946.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.136
• Publications: 0 publications found

Genes affected

ENSG00000303117 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.188 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000791946.1. 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
	ENSG00000303117	ENST00000791946.1		n.261-4038C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.143 AC: 21714 AN: 151730 Hom.: 1839 Cov.: 29

Gnomad AFR AF: 0.0947

Gnomad AMI AF: 0.131

Gnomad AMR AF: 0.106

Gnomad ASJ AF: 0.294

Gnomad EAS AF: 0.00233

Gnomad SAS AF: 0.0989

Gnomad FIN AF: 0.114

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.191

Gnomad OTH AF: 0.155

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

GnomAD4 genome AF: 0.143 AC: 21717 AN: 151850 Hom.: 1840 Cov.: 29 AF XY: 0.136 AC XY: 10074 AN XY: 74182

African (AFR) AF: 0.0948 AC: 3927 AN: 41420

American (AMR) AF: 0.105 AC: 1609 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.294 AC: 1020 AN: 3466

East Asian (EAS) AF: 0.00233 AC: 12 AN: 5140

South Asian (SAS) AF: 0.0984 AC: 471 AN: 4788

European-Finnish (FIN) AF: 0.114 AC: 1204 AN: 10534

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

European-Non Finnish (NFE) AF: 0.191 AC: 12968 AN: 67938

Other (OTH) AF: 0.153 AC: 323 AN: 2106

Alfa AF: 0.162 Hom.: 282

Bravo AF: 0.143

Asia WGS AF: 0.0620 AC: 217 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.0
DANN	Benign	0.69
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs62094879; hg19: chr18-55496305;