ENST00000572864.6:n.203+429G>A

Variant names:

• chr17-47072043-C-T
• rs4074249
• ENST00000572864.6:n.203+429G>A

Variant summary

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

The ENST00000572864.6(ENSG00000262879):​n.203+429G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.454 in 151,824 control chromosomes in the GnomAD database, including 16,223 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 0.45 (16223 hom., cov: 30)
• Consequence: ENSG00000262879 ENST00000572864.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.103
• Publications: 5 publications found

Genes affected

ENSG00000262879 (HGNC:58690):

ENSG00000294414 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.512 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101927060	XR_001753104.3	n.540-393G>A		intron_variant	Intron 2 of 8
LOC101927060	XR_001753117.2	n.540-393G>A		intron_variant	Intron 2 of 8
LOC101927060	XR_001753120.2	n.540-393G>A		intron_variant	Intron 2 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000262879	ENST00000572864.6	n.203+429G>A		intron_variant	Intron 2 of 2	3
ENSG00000262879	ENST00000573341.6	n.502+429G>A		intron_variant	Intron 2 of 2	2
ENSG00000262879	ENST00000576938.2	n.196-393G>A		intron_variant	Intron 2 of 2	5

Frequencies

GnomAD3 genomes AF: 0.454 AC: 68861 AN: 151708 Hom.: 16211 Cov.: 30

Gnomad AFR AF: 0.340

Gnomad AMI AF: 0.479

Gnomad AMR AF: 0.461

Gnomad ASJ AF: 0.625

Gnomad EAS AF: 0.265

Gnomad SAS AF: 0.488

Gnomad FIN AF: 0.507

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.517

Gnomad OTH AF: 0.438

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

GnomAD4 genome AF: 0.454 AC: 68898 AN: 151824 Hom.: 16223 Cov.: 30 AF XY: 0.454 AC XY: 33725 AN XY: 74220

African (AFR) AF: 0.340 AC: 14046 AN: 41328

American (AMR) AF: 0.461 AC: 7044 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.625 AC: 2167 AN: 3468

East Asian (EAS) AF: 0.265 AC: 1371 AN: 5174

South Asian (SAS) AF: 0.489 AC: 2352 AN: 4810

European-Finnish (FIN) AF: 0.507 AC: 5356 AN: 10560

Middle Eastern (MID) AF: 0.422 AC: 124 AN: 294

European-Non Finnish (NFE) AF: 0.517 AC: 35081 AN: 67912

Other (OTH) AF: 0.439 AC: 924 AN: 2104

Alfa AF: 0.363 Hom.: 1023

Bravo AF: 0.444

Asia WGS AF: 0.413 AC: 1434 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.1
DANN	Benign	0.87
PhyloP100		-0.10

Splicing

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

Other links and lift over

dbSNP: rs4074249; hg19: chr17-45149409;