rs2353398

Variant names:

• chr4-144601606-T-A
• rs2353398
• ENST00000649263.1:n.328-185628A>T

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 9 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=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.87 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000649263.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000285713	ENST00000649263.1		n.328-185628A>T		intron	N/A	ENSP00000497507.1	A0A3B3ISY7
	ENSG00000285783	ENST00000650526.1		n.222+153551A>T		intron	N/A

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

African (AFR) AF: 0.878 AC: 35430 AN: 40366

American (AMR) AF: 0.607 AC: 9149 AN: 15078

Ashkenazi Jewish (ASJ) AF: 0.559 AC: 1937 AN: 3468

East Asian (EAS) AF: 0.751 AC: 3786 AN: 5038

South Asian (SAS) AF: 0.811 AC: 3859 AN: 4760

European-Finnish (FIN) AF: 0.638 AC: 6401 AN: 10028

Middle Eastern (MID) AF: 0.551 AC: 161 AN: 292

European-Non Finnish (NFE) AF: 0.531 AC: 35936 AN: 67738

Other (OTH) AF: 0.615 AC: 1278 AN: 2078

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.4
DANN	Benign	0.62
PhyloP100		-1.4

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2353398;

hg19: chr4-145522758;