4-144775888-C-T

Variant names:

• chr4-144775888-C-T
• rs2353934
• ENST00000649263.1:n.327+288684G>A

Variant summary

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

The ENST00000649263.1(ENSG00000285713):​n.327+288684G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.194 in 152,042 control chromosomes in the GnomAD database, including 3,661 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 0.19 (3661 hom., cov: 32)
• Consequence: ENSG00000285713 ENST00000649263.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.835
• Publications: 4 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=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.332 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.327+288684G>A		intron	N/A	ENSP00000497507.1	A0A3B3ISY7
	ENSG00000285783	ENST00000650526.1		n.94-20603G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.194 AC: 29448 AN: 151924 Hom.: 3645 Cov.: 32

Gnomad AFR AF: 0.337

Gnomad AMI AF: 0.0713

Gnomad AMR AF: 0.231

Gnomad ASJ AF: 0.180

Gnomad EAS AF: 0.298

Gnomad SAS AF: 0.232

Gnomad FIN AF: 0.118

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.103

Gnomad OTH AF: 0.169

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

GnomAD4 genome AF: 0.194 AC: 29528 AN: 152042 Hom.: 3661 Cov.: 32 AF XY: 0.196 AC XY: 14606 AN XY: 74346

African (AFR) AF: 0.337 AC: 13946 AN: 41418

American (AMR) AF: 0.232 AC: 3547 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.180 AC: 625 AN: 3466

East Asian (EAS) AF: 0.297 AC: 1532 AN: 5152

South Asian (SAS) AF: 0.234 AC: 1129 AN: 4824

European-Finnish (FIN) AF: 0.118 AC: 1252 AN: 10578

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.103 AC: 7036 AN: 68004

Other (OTH) AF: 0.176 AC: 371 AN: 2112

Alfa AF: 0.137 Hom.: 5650

Bravo AF: 0.205

Asia WGS AF: 0.287 AC: 996 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.65
DANN	Benign	0.41
PhyloP100		-0.83

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: rs2353934;

hg19: chr4-145697040;