chr15-46347610-G-A

Variant names:

• chr15-46347610-G-A
• rs4775302
• ENST00000669454.1:n.391-3744G>A

Variant summary

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

The ENST00000669454.1(ENSG00000287020):​n.391-3744G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.489 in 151,906 control chromosomes in the GnomAD database, including 18,868 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 0.49 (18868 hom., cov: 32)
• Consequence: ENSG00000287020 ENST00000669454.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.38
• Publications: 27 publications found

Genes affected

ENSG00000287020 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.544 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
ENSG00000287020	ENST00000669454.1	n.391-3744G>A		intron_variant	Intron 2 of 2
ENSG00000305466	ENST00000811159.1	n.204-26863G>A		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.489 AC: 74206 AN: 151788 Hom.: 18862 Cov.: 32

Gnomad AFR AF: 0.446

Gnomad AMI AF: 0.615

Gnomad AMR AF: 0.426

Gnomad ASJ AF: 0.588

Gnomad EAS AF: 0.207

Gnomad SAS AF: 0.403

Gnomad FIN AF: 0.491

Gnomad MID AF: 0.598

Gnomad NFE AF: 0.549

Gnomad OTH AF: 0.499

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

GnomAD4 genome AF: 0.489 AC: 74256 AN: 151906 Hom.: 18868 Cov.: 32 AF XY: 0.482 AC XY: 35750 AN XY: 74216

African (AFR) AF: 0.446 AC: 18476 AN: 41420

American (AMR) AF: 0.426 AC: 6502 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.588 AC: 2039 AN: 3470

East Asian (EAS) AF: 0.207 AC: 1065 AN: 5154

South Asian (SAS) AF: 0.404 AC: 1942 AN: 4806

European-Finnish (FIN) AF: 0.491 AC: 5153 AN: 10504

Middle Eastern (MID) AF: 0.602 AC: 177 AN: 294

European-Non Finnish (NFE) AF: 0.549 AC: 37295 AN: 67970

Other (OTH) AF: 0.496 AC: 1047 AN: 2110

Alfa AF: 0.520 Hom.: 51111

Bravo AF: 0.481

Asia WGS AF: 0.301 AC: 1048 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.11
DANN	Benign	0.39
PhyloP100		-2.4

Splicing

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

Other links and lift over

dbSNP: rs4775302; hg19: chr15-46639808; COSMIC: COSV71840654;