17-49374901-C-T

Position:

• chr17-49374901-C-T

Variant summary

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

The ENST00000576461.1(ENSG00000262039):​n.270+1815C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0659 in 122,764 control chromosomes in the GnomAD database, including 314 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 0.066 (314 hom., cov: 22)
• Consequence: ENST00000576461.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.65

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0916 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZNF652-AS1	NR_110883.1	n.244-409C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000576461.1	n.270+1815C>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.0660 AC: 8099 AN: 122746 Hom.: 314 Cov.: 22

Gnomad AFR AF: 0.0350

Gnomad AMI AF: 0.0289

Gnomad AMR AF: 0.0805

Gnomad ASJ AF: 0.151

Gnomad EAS AF: 0.000238

Gnomad SAS AF: 0.0996

Gnomad FIN AF: 0.0342

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.0788

Gnomad OTH AF: 0.0753

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

GnomAD4 genome AF: 0.0659 AC: 8094 AN: 122764 Hom.: 314 Cov.: 22 AF XY: 0.0646 AC XY: 3682 AN XY: 56982

Gnomad4 AFR AF: 0.0350

Gnomad4 AMR AF: 0.0805

Gnomad4 ASJ AF: 0.151

Gnomad4 EAS AF: 0.000239

Gnomad4 SAS AF: 0.0997

Gnomad4 FIN AF: 0.0342

Gnomad4 NFE AF: 0.0788

Gnomad4 OTH AF: 0.0744

Alfa AF: 0.0630 Hom.: 46

Bravo AF: 0.0578

Asia WGS AF: 0.0390 AC: 136 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.52
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11655191; hg19: chr17-47452263;