17-47072043-C-T

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 ENST00000573341.6(ENSG00000262879):​n.502+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 ENST00000573341.6 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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000573341.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000262879	ENST00000572864.6	TSL:3	n.203+429G>A		intron	N/A
	ENSG00000262879	ENST00000573341.6	TSL:2	n.502+429G>A		intron	N/A
	ENSG00000262879	ENST00000576938.2	TSL:5	n.196-393G>A		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs4074249;

hg19: chr17-45149409;