14-62486405-G-C

Variant names:

• chr14-62486405-G-C
• rs17100010
• ENST00000743723.1:n.587-17639G>C

Variant summary

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

The ENST00000743723.1(ENSG00000296937):​n.587-17639G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.352 in 151,970 control chromosomes in the GnomAD database, including 9,653 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 0.35 (9653 hom., cov: 32)
• Consequence: ENSG00000296937 ENST00000743723.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.362
• Publications: 1 publications found

Genes affected

ENSG00000296937 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.381 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000743723.1. 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
	ENSG00000296937	ENST00000743723.1		n.587-17639G>C		intron	N/A
	ENSG00000296937	ENST00000743724.1		n.588-17639G>C		intron	N/A
	ENSG00000296937	ENST00000743725.1		n.333-17636G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.352 AC: 53507 AN: 151852 Hom.: 9648 Cov.: 32

Gnomad AFR AF: 0.380

Gnomad AMI AF: 0.492

Gnomad AMR AF: 0.290

Gnomad ASJ AF: 0.494

Gnomad EAS AF: 0.395

Gnomad SAS AF: 0.242

Gnomad FIN AF: 0.348

Gnomad MID AF: 0.440

Gnomad NFE AF: 0.345

Gnomad OTH AF: 0.365

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

GnomAD4 genome AF: 0.352 AC: 53533 AN: 151970 Hom.: 9653 Cov.: 32 AF XY: 0.349 AC XY: 25932 AN XY: 74282

African (AFR) AF: 0.380 AC: 15748 AN: 41424

American (AMR) AF: 0.289 AC: 4410 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.494 AC: 1716 AN: 3472

East Asian (EAS) AF: 0.395 AC: 2043 AN: 5168

South Asian (SAS) AF: 0.241 AC: 1165 AN: 4828

European-Finnish (FIN) AF: 0.348 AC: 3676 AN: 10568

Middle Eastern (MID) AF: 0.446 AC: 131 AN: 294

European-Non Finnish (NFE) AF: 0.345 AC: 23429 AN: 67932

Other (OTH) AF: 0.363 AC: 768 AN: 2114

Alfa AF: 0.352 Hom.: 1150

Bravo AF: 0.352

Asia WGS AF: 0.337 AC: 1170 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.3
DANN	Benign	0.37
PhyloP100		-0.36

Splicing

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

Other links and lift over

dbSNP: rs17100010; hg19: chr14-62953123;