chr15-46604485-C-T

Variant names:

• chr15-46604485-C-T
• rs526439
• ENST00000661853.1:n.46-55730C>T

Variant summary

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

The ENST00000661853.1(ENSG00000287704):​n.46-55730C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.199 in 152,046 control chromosomes in the GnomAD database, including 4,911 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 (4911 hom., cov: 32)
• Consequence: ENSG00000287704 ENST00000661853.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.332
• Publications: 0 publications found

Genes affected

ENSG00000287704 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.441 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
ENSG00000287704	ENST00000661853.1	n.46-55730C>T		intron_variant	Intron 1 of 1
ENSG00000287704	ENST00000686120.1	n.191+26144C>T		intron_variant	Intron 2 of 2
ENSG00000287704	ENST00000736459.1	n.181+26144C>T		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.199 AC: 30212 AN: 151928 Hom.: 4897 Cov.: 32

Gnomad AFR AF: 0.446

Gnomad AMI AF: 0.0570

Gnomad AMR AF: 0.110

Gnomad ASJ AF: 0.104

Gnomad EAS AF: 0.0214

Gnomad SAS AF: 0.101

Gnomad FIN AF: 0.0791

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.116

Gnomad OTH AF: 0.175

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

GnomAD4 genome AF: 0.199 AC: 30271 AN: 152046 Hom.: 4911 Cov.: 32 AF XY: 0.194 AC XY: 14401 AN XY: 74340

African (AFR) AF: 0.446 AC: 18488 AN: 41446

American (AMR) AF: 0.110 AC: 1678 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.104 AC: 362 AN: 3472

East Asian (EAS) AF: 0.0217 AC: 112 AN: 5166

South Asian (SAS) AF: 0.101 AC: 489 AN: 4818

European-Finnish (FIN) AF: 0.0791 AC: 838 AN: 10590

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.115 AC: 7851 AN: 67976

Other (OTH) AF: 0.175 AC: 369 AN: 2112

Alfa AF: 0.222 Hom.: 2875

Bravo AF: 0.212

Asia WGS AF: 0.106 AC: 368 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.3
DANN	Benign	0.35
PhyloP100		-0.33

Splicing

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

Other links and lift over

dbSNP: rs526439; hg19: chr15-46896683;