rs3764506

Variant names:

• chr18-74292238-C-T
• rs3764506
• ENST00000849951.1:n.26C>T

Variant summary

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

The ENST00000849951.1(ENSG00000286529):​n.26C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0158 in 152,296 control chromosomes in the GnomAD database, including 113 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 0.016 (113 hom., cov: 33)
• Consequence: ENSG00000286529 ENST00000849951.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04
• Publications: 1 publications found

Genes affected

ENSG00000286529 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.175 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000286529	ENST00000849951.1	n.26C>T		non_coding_transcript_exon_variant	Exon 1 of 3
ENSG00000286529	ENST00000849952.1	n.19C>T		non_coding_transcript_exon_variant	Exon 1 of 2
ENSG00000286529	ENST00000849953.1	n.11C>T		non_coding_transcript_exon_variant	Exon 1 of 2

Frequencies

GnomAD3 genomes AF: 0.0158 AC: 2407 AN: 152178 Hom.: 113 Cov.: 33

Gnomad AFR AF: 0.0162

Gnomad AMI AF: 0.0263

Gnomad AMR AF: 0.0171

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.184

Gnomad SAS AF: 0.00993

Gnomad FIN AF: 0.0134

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.00406

Gnomad OTH AF: 0.0148

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

GnomAD4 genome AF: 0.0158 AC: 2412 AN: 152296 Hom.: 113 Cov.: 33 AF XY: 0.0169 AC XY: 1262 AN XY: 74466

African (AFR) AF: 0.0163 AC: 678 AN: 41560

American (AMR) AF: 0.0172 AC: 263 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3472

East Asian (EAS) AF: 0.184 AC: 953 AN: 5170

South Asian (SAS) AF: 0.00973 AC: 47 AN: 4828

European-Finnish (FIN) AF: 0.0134 AC: 142 AN: 10622

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.00406 AC: 276 AN: 68024

Other (OTH) AF: 0.0137 AC: 29 AN: 2110

Alfa AF: 0.0104 Hom.: 3

Bravo AF: 0.0186

Asia WGS AF: 0.0670 AC: 233 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	0.47
DANN	Benign	0.79
PhyloP100		-1.0
PromoterAI		0.0094	Neutral

Splicing

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

Other links and lift over

dbSNP: rs3764506; hg19: chr18-71959473;