chr4-187270152-C-A

Variant names:

• chr4-187270152-C-A
• rs4478239
• ENST00000795547.1:n.521-3830G>T

Variant summary

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

The ENST00000795547.1(ENSG00000250658):​n.521-3830G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.903 in 150,898 control chromosomes in the GnomAD database, including 61,582 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 (61582 hom., cov: 26)
• Consequence: ENSG00000250658 ENST00000795547.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.124
• Publications: 12 publications found

Genes affected

ENSG00000250658 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.926 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
ENSG00000250658	ENST00000795547.1	n.521-3830G>T		intron_variant	Intron 4 of 6
ENSG00000250658	ENST00000795548.1	n.582-3830G>T		intron_variant	Intron 3 of 5
ENSG00000250658	ENST00000795549.1	n.580-3830G>T		intron_variant	Intron 3 of 5

Frequencies

GnomAD3 genomes AF: 0.903 AC: 136145 AN: 150782 Hom.: 61529 Cov.: 26

Gnomad AFR AF: 0.934

Gnomad AMI AF: 0.932

Gnomad AMR AF: 0.904

Gnomad ASJ AF: 0.872

Gnomad EAS AF: 0.924

Gnomad SAS AF: 0.866

Gnomad FIN AF: 0.872

Gnomad MID AF: 0.901

Gnomad NFE AF: 0.891

Gnomad OTH AF: 0.900

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

GnomAD4 genome AF: 0.903 AC: 136256 AN: 150898 Hom.: 61582 Cov.: 26 AF XY: 0.901 AC XY: 66239 AN XY: 73544

African (AFR) AF: 0.934 AC: 38368 AN: 41076

American (AMR) AF: 0.905 AC: 13713 AN: 15158

Ashkenazi Jewish (ASJ) AF: 0.872 AC: 3019 AN: 3462

East Asian (EAS) AF: 0.924 AC: 4723 AN: 5110

South Asian (SAS) AF: 0.866 AC: 4113 AN: 4752

European-Finnish (FIN) AF: 0.872 AC: 8947 AN: 10266

Middle Eastern (MID) AF: 0.898 AC: 264 AN: 294

European-Non Finnish (NFE) AF: 0.891 AC: 60379 AN: 67782

Other (OTH) AF: 0.901 AC: 1884 AN: 2090

Alfa AF: 0.896 Hom.: 111630

Bravo AF: 0.908

Asia WGS AF: 0.923 AC: 3198 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.65
DANN	Benign	0.42
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs4478239; hg19: chr4-188191306;