17-14463621-G-C

Position:

• chr17-14463621-G-C

Variant summary

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

The ENST00000700765.1(ENSG00000230647):​n.146G>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.113 in 152,160 control chromosomes in the GnomAD database, including 2,493 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 0.11 (2493 hom., cov: 33)
• Consequence: ENSG00000230647 ENST00000700765.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.108

Genes affected

ENSG00000230647 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.331 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.14463621G>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000230647	ENST00000700765.1	n.146G>C		non_coding_transcript_exon_variant	3/4

Frequencies

GnomAD3 genomes AF: 0.113 AC: 17169 AN: 152042 Hom.: 2476 Cov.: 33

Gnomad AFR AF: 0.335

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.0562

Gnomad ASJ AF: 0.0332

Gnomad EAS AF: 0.187

Gnomad SAS AF: 0.0935

Gnomad FIN AF: 0.000753

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0105

Gnomad OTH AF: 0.0856

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

GnomAD4 genome AF: 0.113 AC: 17248 AN: 152160 Hom.: 2493 Cov.: 33 AF XY: 0.112 AC XY: 8366 AN XY: 74394

Gnomad4 AFR AF: 0.336

Gnomad4 AMR AF: 0.0565

Gnomad4 ASJ AF: 0.0332

Gnomad4 EAS AF: 0.187

Gnomad4 SAS AF: 0.0930

Gnomad4 FIN AF: 0.000753

Gnomad4 NFE AF: 0.0105

Gnomad4 OTH AF: 0.0881

Alfa AF: 0.0161 Hom.: 39

Bravo AF: 0.126

Asia WGS AF: 0.143 AC: 498 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.7
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4791580; hg19: chr17-14366938;