4-28663346-T-C

Variant names:

• chr4-28663346-T-C
• rs6815271
• ENST00000730159.1:n.145+15595A>G

Variant summary

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

The ENST00000730159.1(ENSG00000286141):​n.145+15595A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.9 in 152,242 control chromosomes in the GnomAD database, including 61,889 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 0.90 (61889 hom., cov: 32)
• Consequence: ENSG00000286141 ENST00000730159.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.96
• Publications: 2 publications found

Genes affected

ENSG00000286141 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.964 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
ENSG00000286141	ENST00000730159.1	n.145+15595A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.900 AC: 136929 AN: 152124 Hom.: 61831 Cov.: 32

Gnomad AFR AF: 0.972

Gnomad AMI AF: 0.873

Gnomad AMR AF: 0.891

Gnomad ASJ AF: 0.887

Gnomad EAS AF: 0.985

Gnomad SAS AF: 0.930

Gnomad FIN AF: 0.922

Gnomad MID AF: 0.899

Gnomad NFE AF: 0.848

Gnomad OTH AF: 0.887

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

GnomAD4 genome AF: 0.900 AC: 137047 AN: 152242 Hom.: 61889 Cov.: 32 AF XY: 0.904 AC XY: 67264 AN XY: 74434

African (AFR) AF: 0.972 AC: 40418 AN: 41580

American (AMR) AF: 0.892 AC: 13618 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.887 AC: 3078 AN: 3472

East Asian (EAS) AF: 0.985 AC: 5090 AN: 5170

South Asian (SAS) AF: 0.930 AC: 4484 AN: 4824

European-Finnish (FIN) AF: 0.922 AC: 9775 AN: 10598

Middle Eastern (MID) AF: 0.901 AC: 265 AN: 294

European-Non Finnish (NFE) AF: 0.848 AC: 57651 AN: 68012

Other (OTH) AF: 0.888 AC: 1872 AN: 2108

Alfa AF: 0.865 Hom.: 25488

Bravo AF: 0.899

Asia WGS AF: 0.958 AC: 3332 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.14
DANN	Benign	0.66
PhyloP100		-3.0

Splicing

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

Other links and lift over

dbSNP: rs6815271; hg19: chr4-28664968;