rs2353398

Positions:

• chr4-144601606-T-A
• chr4-144601606-T-C

Variant summary

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

The ENST00000649263.1(ENSG00000285713):​n.328-185628A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.657 in 149,750 control chromosomes in the GnomAD database, including 34,045 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 0.66 (34045 hom., cov: 27)
• Consequence: ENSG00000285713 ENST00000649263.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.45

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 = 0.87 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.144601606T>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000285713	ENST00000649263.1	n.328-185628A>T		intron_variant				ENSP00000497507.1
ENSG00000285783	ENST00000650526.1	n.222+153551A>T		intron_variant

Frequencies

GnomAD3 genomes AF: 0.657 AC: 98350 AN: 149678 Hom.: 34009 Cov.: 27

Gnomad AFR AF: 0.878

Gnomad AMI AF: 0.542

Gnomad AMR AF: 0.606

Gnomad ASJ AF: 0.559

Gnomad EAS AF: 0.751

Gnomad SAS AF: 0.811

Gnomad FIN AF: 0.638

Gnomad MID AF: 0.564

Gnomad NFE AF: 0.531

Gnomad OTH AF: 0.614

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

GnomAD4 genome AF: 0.657 AC: 98427 AN: 149750 Hom.: 34045 Cov.: 27 AF XY: 0.664 AC XY: 48389 AN XY: 72878

Gnomad4 AFR AF: 0.878

Gnomad4 AMR AF: 0.607

Gnomad4 ASJ AF: 0.559

Gnomad4 EAS AF: 0.751

Gnomad4 SAS AF: 0.811

Gnomad4 FIN AF: 0.638

Gnomad4 NFE AF: 0.531

Gnomad4 OTH AF: 0.615

Alfa AF: 0.489 Hom.: 1473

Bravo AF: 0.663

Asia WGS AF: 0.809 AC: 2812 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	1.4
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2353398; hg19: chr4-145522758;