4-144404378-G-T

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000285713 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377462	XR_939272.3	n.314+11525C>A		intron_variant	Intron 3 of 7
LOC105377462	XR_939273.3	n.240+11525C>A		intron_variant	Intron 2 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000285713	ENST00000649263.1	n.*43+11525C>A		intron_variant	Intron 5 of 8			ENSP00000497507.1
ENSG00000285783	ENST00000648340.1	n.214+11525C>A		intron_variant	Intron 2 of 5
ENSG00000285783	ENST00000650526.1	n.298+11525C>A		intron_variant	Intron 3 of 14

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

Gnomad4 AFR AF: 0.212

Gnomad4 AMR AF: 0.511

Gnomad4 ASJ AF: 0.551

Gnomad4 EAS AF: 0.538

Gnomad4 SAS AF: 0.615

Gnomad4 FIN AF: 0.646

Gnomad4 NFE AF: 0.597

Gnomad4 OTH AF: 0.513

Alfa AF: 0.559 Hom.: 12045

Bravo AF: 0.459

Asia WGS AF: 0.503 AC: 1747 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1394999; hg19: chr4-145325530;