4-144594617-A-C

Variant names:

• chr4-144594617-A-C
• rs1542726
• ENST00000649263.1:n.328-178639T>G

Variant summary

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

The ENST00000649263.1(ENSG00000285713):​n.328-178639T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.682 in 152,034 control chromosomes in the GnomAD database, including 36,731 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 0.68 (36731 hom., cov: 31)
• Consequence: ENSG00000285713 ENST00000649263.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.941
• Publications: 5 publications found

Genes affected

ENSG00000285713 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.862 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
ENSG00000285713	ENST00000649263.1	n.328-178639T>G		intron_variant	Intron 4 of 8			ENSP00000497507.1
ENSG00000285783	ENST00000650526.1	n.222+160540T>G		intron_variant	Intron 2 of 14

Frequencies

GnomAD3 genomes AF: 0.682 AC: 103642 AN: 151916 Hom.: 36676 Cov.: 31

Gnomad AFR AF: 0.869

Gnomad AMI AF: 0.542

Gnomad AMR AF: 0.648

Gnomad ASJ AF: 0.541

Gnomad EAS AF: 0.623

Gnomad SAS AF: 0.848

Gnomad FIN AF: 0.680

Gnomad MID AF: 0.601

Gnomad NFE AF: 0.581

Gnomad OTH AF: 0.622

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

GnomAD4 genome AF: 0.682 AC: 103762 AN: 152034 Hom.: 36731 Cov.: 31 AF XY: 0.688 AC XY: 51142 AN XY: 74322

African (AFR) AF: 0.869 AC: 36044 AN: 41476

American (AMR) AF: 0.649 AC: 9914 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.541 AC: 1876 AN: 3470

East Asian (EAS) AF: 0.624 AC: 3220 AN: 5160

South Asian (SAS) AF: 0.848 AC: 4088 AN: 4818

European-Finnish (FIN) AF: 0.680 AC: 7182 AN: 10568

Middle Eastern (MID) AF: 0.599 AC: 176 AN: 294

European-Non Finnish (NFE) AF: 0.581 AC: 39454 AN: 67944

Other (OTH) AF: 0.623 AC: 1314 AN: 2110

Alfa AF: 0.632 Hom.: 6339

Bravo AF: 0.677

Asia WGS AF: 0.787 AC: 2739 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.20
DANN	Benign	0.77
PhyloP100		-0.94

Splicing

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

Other links and lift over

dbSNP: rs1542726; hg19: chr4-145515769;