4-144529807-A-G

Variant names:

• chr4-144529807-A-G
• rs1512285
• ENST00000649263.1:n.328-113829T>C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000649263.1(ENSG00000285713):​n.328-113829T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.65 in 151,928 control chromosomes in the GnomAD database, including 33,227 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 0.65 (33227 hom., cov: 31)
• Consequence: ENSG00000285713 ENST00000649263.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.94

Genes affected

ENSG00000285713 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.3).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.823 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377462	XR_939272.3	n.165-30287T>C		intron_variant	Intron 1 of 7
LOC105377462	XR_939273.3	n.164+32177T>C		intron_variant	Intron 1 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000285713	ENST00000649263.1	n.328-113829T>C		intron_variant	Intron 4 of 8			ENSP00000497507.1
ENSG00000285783	ENST00000650526.1	n.223-113829T>C		intron_variant	Intron 2 of 14

Frequencies

GnomAD3 genomes AF: 0.650 AC: 98723 AN: 151810 Hom.: 33190 Cov.: 31

Gnomad AFR AF: 0.813

Gnomad AMI AF: 0.524

Gnomad AMR AF: 0.640

Gnomad ASJ AF: 0.520

Gnomad EAS AF: 0.618

Gnomad SAS AF: 0.845

Gnomad FIN AF: 0.617

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.558

Gnomad OTH AF: 0.604

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

GnomAD4 genome AF: 0.650 AC: 98821 AN: 151928 Hom.: 33227 Cov.: 31 AF XY: 0.655 AC XY: 48662 AN XY: 74250

Gnomad4 AFR AF: 0.813

Gnomad4 AMR AF: 0.641

Gnomad4 ASJ AF: 0.520

Gnomad4 EAS AF: 0.618

Gnomad4 SAS AF: 0.845

Gnomad4 FIN AF: 0.617

Gnomad4 NFE AF: 0.558

Gnomad4 OTH AF: 0.604

Alfa AF: 0.611 Hom.: 14160

Bravo AF: 0.648

Asia WGS AF: 0.768 AC: 2671 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.30
CADD	Benign	21
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1512285; hg19: chr4-145450959;