ENST00000644129.1:n.281+24933A>G

Variant names:

• chr6-105805124-T-C
• rs1355023
• ENST00000644129.1:n.281+24933A>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000644129.1(ENSG00000284999):​n.281+24933A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.36 in 152,048 control chromosomes in the GnomAD database, including 10,447 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 0.36 (10447 hom., cov: 33)
• Consequence: ENSG00000284999 ENST00000644129.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.112

Genes affected

ENSG00000284999 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.484 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000284999	ENST00000644129.1	n.281+24933A>G		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.360 AC: 54642 AN: 151930 Hom.: 10433 Cov.: 33

Gnomad AFR AF: 0.490

Gnomad AMI AF: 0.326

Gnomad AMR AF: 0.253

Gnomad ASJ AF: 0.276

Gnomad EAS AF: 0.376

Gnomad SAS AF: 0.388

Gnomad FIN AF: 0.338

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.310

Gnomad OTH AF: 0.339

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

GnomAD4 genome AF: 0.360 AC: 54703 AN: 152048 Hom.: 10447 Cov.: 33 AF XY: 0.359 AC XY: 26677 AN XY: 74306

Gnomad4 AFR AF: 0.490

Gnomad4 AMR AF: 0.253

Gnomad4 ASJ AF: 0.276

Gnomad4 EAS AF: 0.375

Gnomad4 SAS AF: 0.389

Gnomad4 FIN AF: 0.338

Gnomad4 NFE AF: 0.310

Gnomad4 OTH AF: 0.339

Alfa AF: 0.313 Hom.: 7889

Bravo AF: 0.358

Asia WGS AF: 0.378 AC: 1311 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	4.5
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1355023; hg19: chr6-106252999;