17-14463621-G-C

Variant names:

• chr17-14463621-G-C
• rs4791580
• ENST00000700765.2:n.164G>C

Variant summary

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

The ENST00000700765.2(ENSG00000230647):​n.164G>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 ENST00000700765.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.108
• Publications: 1 publications found

Genes affected

ENSG00000230647 (HGNC:58488):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000700765.2. 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
	ENSG00000230647	ENST00000700765.2		n.164G>C		non_coding_transcript_exon	Exon 3 of 4
	ENSG00000230647	ENST00000822015.1		n.239G>C		non_coding_transcript_exon	Exon 3 of 4
	ENSG00000230647	ENST00000822016.1		n.300G>C		non_coding_transcript_exon	Exon 4 of 6

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

African (AFR) AF: 0.336 AC: 13928 AN: 41450

American (AMR) AF: 0.0565 AC: 865 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0332 AC: 115 AN: 3468

East Asian (EAS) AF: 0.187 AC: 965 AN: 5154

South Asian (SAS) AF: 0.0930 AC: 449 AN: 4830

European-Finnish (FIN) AF: 0.000753 AC: 8 AN: 10618

Middle Eastern (MID) AF: 0.0544 AC: 16 AN: 294

European-Non Finnish (NFE) AF: 0.0105 AC: 714 AN: 68020

Other (OTH) AF: 0.0881 AC: 186 AN: 2112

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.7
DANN	Benign	0.61
PhyloP100		-0.11

Splicing

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

Other links and lift over

dbSNP: rs4791580; hg19: chr17-14366938;