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. The variant received -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
• Publications: 7 publications found

Genes affected

ENSG00000284999 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000644129.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000284999	ENST00000644129.1		n.281+24933A>G		intron	N/A
	ENSG00000284999	ENST00000744159.1		n.374+24933A>G		intron	N/A

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

African (AFR) AF: 0.490 AC: 20315 AN: 41458

American (AMR) AF: 0.253 AC: 3864 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.276 AC: 956 AN: 3470

East Asian (EAS) AF: 0.375 AC: 1941 AN: 5170

South Asian (SAS) AF: 0.389 AC: 1877 AN: 4826

European-Finnish (FIN) AF: 0.338 AC: 3562 AN: 10552

Middle Eastern (MID) AF: 0.279 AC: 82 AN: 294

European-Non Finnish (NFE) AF: 0.310 AC: 21094 AN: 67978

Other (OTH) AF: 0.339 AC: 715 AN: 2112

Alfa AF: 0.331 Hom.: 13793

Bravo AF: 0.358

Asia WGS AF: 0.378 AC: 1311 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	4.5
DANN	Benign	0.57
PhyloP100		0.11

Splicing

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

Other links and lift over

dbSNP: rs1355023; hg19: chr6-106252999;