4-144596426-C-T

Variant names:

• chr4-144596426-C-T
• rs2353397
• ENST00000649263.1:n.328-180448G>A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000649263.1(ENSG00000285713):​n.328-180448G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.674 in 152,082 control chromosomes in the GnomAD database, including 36,121 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 0.67 (36121 hom., cov: 31)
• Consequence: ENSG00000285713 ENST00000649263.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.247

Genes affected

ENSG00000285713 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.868 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.328-180448G>A		intron_variant	Intron 4 of 8			ENSP00000497507.1
ENSG00000285783	ENST00000650526.1	n.222+158731G>A		intron_variant	Intron 2 of 14

Frequencies

GnomAD3 genomes AF: 0.673 AC: 102324 AN: 151964 Hom.: 36074 Cov.: 31

Gnomad AFR AF: 0.876

Gnomad AMI AF: 0.491

Gnomad AMR AF: 0.647

Gnomad ASJ AF: 0.553

Gnomad EAS AF: 0.754

Gnomad SAS AF: 0.819

Gnomad FIN AF: 0.630

Gnomad MID AF: 0.631

Gnomad NFE AF: 0.557

Gnomad OTH AF: 0.608

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

GnomAD4 genome AF: 0.674 AC: 102430 AN: 152082 Hom.: 36121 Cov.: 31 AF XY: 0.678 AC XY: 50367 AN XY: 74326

Gnomad4 AFR AF: 0.876

Gnomad4 AMR AF: 0.648

Gnomad4 ASJ AF: 0.553

Gnomad4 EAS AF: 0.755

Gnomad4 SAS AF: 0.819

Gnomad4 FIN AF: 0.630

Gnomad4 NFE AF: 0.557

Gnomad4 OTH AF: 0.608

Alfa AF: 0.612 Hom.: 17575

Bravo AF: 0.677

Asia WGS AF: 0.803 AC: 2792 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.9
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2353397; hg19: chr4-145517578;