3-114219388-C-T

Variant names:

• chr3-114219388-C-T
• rs2399504
• ENST00000481773.2:n.238+4838C>T

Variant summary

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

The ENST00000493033.1(ENSG00000241490):​n.160+4838C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.177 in 152,178 control chromosomes in the GnomAD database, including 2,863 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 0.18 (2863 hom., cov: 33)
• Consequence: ENSG00000241490 ENST00000493033.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.228
• Publications: 7 publications found

Genes affected

ENSG00000241490 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.299 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000493033.1. 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
	ENSG00000241490	ENST00000481773.2	TSL:3	n.238+4838C>T		intron	N/A
	ENSG00000241490	ENST00000493033.1	TSL:2	n.160+4838C>T		intron	N/A
	ENSG00000241490	ENST00000779676.1		n.341+4838C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.177 AC: 26978 AN: 152060 Hom.: 2856 Cov.: 33

Gnomad AFR AF: 0.0801

Gnomad AMI AF: 0.225

Gnomad AMR AF: 0.306

Gnomad ASJ AF: 0.170

Gnomad EAS AF: 0.238

Gnomad SAS AF: 0.122

Gnomad FIN AF: 0.232

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.199

Gnomad OTH AF: 0.176

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

GnomAD4 genome AF: 0.177 AC: 26992 AN: 152178 Hom.: 2863 Cov.: 33 AF XY: 0.181 AC XY: 13458 AN XY: 74394

African (AFR) AF: 0.0798 AC: 3316 AN: 41532

American (AMR) AF: 0.307 AC: 4686 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.170 AC: 590 AN: 3466

East Asian (EAS) AF: 0.239 AC: 1237 AN: 5182

South Asian (SAS) AF: 0.122 AC: 589 AN: 4822

European-Finnish (FIN) AF: 0.232 AC: 2451 AN: 10566

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.199 AC: 13500 AN: 68008

Other (OTH) AF: 0.175 AC: 371 AN: 2114

Alfa AF: 0.169 Hom.: 358

Bravo AF: 0.182

Asia WGS AF: 0.167 AC: 580 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.4
DANN	Benign	0.50
PhyloP100		0.23

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: rs2399504;

hg19: chr3-113938235;