4-144404378-G-T

Variant names:

• chr4-144404378-G-T
• rs1394999
• ENST00000649263.1:n.*43+11525C>A

Variant summary

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

The ENST00000649263.1(ENSG00000285713):​n.*43+11525C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.483 in 151,934 control chromosomes in the GnomAD database, including 19,930 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 0.48 (19930 hom., cov: 31)
• Consequence: ENSG00000285713 ENST00000649263.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0290
• Publications: 3 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=-0.99).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.596 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

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000285713	ENST00000649263.1		n.*43+11525C>A		intron	N/A	ENSP00000497507.1
	ENSG00000285783	ENST00000648340.1		n.214+11525C>A		intron	N/A
	ENSG00000285783	ENST00000650526.1		n.298+11525C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.483 AC: 73384 AN: 151814 Hom.: 19921 Cov.: 31

Gnomad AFR AF: 0.212

Gnomad AMI AF: 0.569

Gnomad AMR AF: 0.511

Gnomad ASJ AF: 0.551

Gnomad EAS AF: 0.538

Gnomad SAS AF: 0.614

Gnomad FIN AF: 0.646

Gnomad MID AF: 0.634

Gnomad NFE AF: 0.597

Gnomad OTH AF: 0.513

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

GnomAD4 genome AF: 0.483 AC: 73416 AN: 151934 Hom.: 19930 Cov.: 31 AF XY: 0.489 AC XY: 36323 AN XY: 74254

African (AFR) AF: 0.212 AC: 8787 AN: 41436

American (AMR) AF: 0.511 AC: 7790 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.551 AC: 1909 AN: 3466

East Asian (EAS) AF: 0.538 AC: 2779 AN: 5164

South Asian (SAS) AF: 0.615 AC: 2960 AN: 4814

European-Finnish (FIN) AF: 0.646 AC: 6822 AN: 10566

Middle Eastern (MID) AF: 0.654 AC: 191 AN: 292

European-Non Finnish (NFE) AF: 0.597 AC: 40577 AN: 67938

Other (OTH) AF: 0.513 AC: 1082 AN: 2110

Alfa AF: 0.554 Hom.: 16573

Bravo AF: 0.459

Asia WGS AF: 0.503 AC: 1747 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.80
DANN	Benign	0.30
PhyloP100		-0.029

Splicing

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

Other links and lift over

dbSNP: rs1394999; hg19: chr4-145325530;