14-20438455-G-C

Variant names:

• chr14-20438455-G-C
• rs2184283
• ENST00000553568.1:n.75-51G>C

Variant summary

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

The ENST00000687238.1(ENSG00000291038):​n.338-198G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.386 in 151,950 control chromosomes in the GnomAD database, including 12,034 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 0.39 (12032 hom., cov: 31)
  • Exomes 𝑓: 0.32 (2 hom.)
• Consequence: ENSG00000291038 ENST00000687238.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.289
• Publications: 4 publications found

Genes affected

ENSG00000259162 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.505 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000687238.1. 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
	ENSG00000259162	ENST00000553568.1	TSL:6	n.75-51G>C		intron	N/A
	ENSG00000291038	ENST00000687238.1		n.338-198G>C		intron	N/A
	ENSG00000291038	ENST00000700970.2		n.337+418G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.386 AC: 58568 AN: 151798 Hom.: 12015 Cov.: 31

Gnomad AFR AF: 0.511

Gnomad AMI AF: 0.255

Gnomad AMR AF: 0.440

Gnomad ASJ AF: 0.230

Gnomad EAS AF: 0.334

Gnomad SAS AF: 0.255

Gnomad FIN AF: 0.370

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.324

Gnomad OTH AF: 0.370

GnomAD4 exome AF: 0.324 AC: 11 AN: 34 Hom.: 2 Cov.: 0 AF XY: 0.150 AC XY: 3 AN XY: 20

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.250 AC: 1 AN: 4

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.333 AC: 10 AN: 30

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.386 AC: 58629 AN: 151916 Hom.: 12032 Cov.: 31 AF XY: 0.386 AC XY: 28654 AN XY: 74260

African (AFR) AF: 0.511 AC: 21139 AN: 41356

American (AMR) AF: 0.441 AC: 6731 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.230 AC: 797 AN: 3468

East Asian (EAS) AF: 0.333 AC: 1718 AN: 5158

South Asian (SAS) AF: 0.254 AC: 1222 AN: 4808

European-Finnish (FIN) AF: 0.370 AC: 3910 AN: 10560

Middle Eastern (MID) AF: 0.289 AC: 85 AN: 294

European-Non Finnish (NFE) AF: 0.324 AC: 22016 AN: 67976

Other (OTH) AF: 0.369 AC: 778 AN: 2110

Alfa AF: 0.188 Hom.: 326

Bravo AF: 0.399

Asia WGS AF: 0.323 AC: 1124 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.3
DANN	Benign	0.46
PhyloP100		0.29

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: rs2184283;

hg19: chr14-20906614;