chr14-20437356-A-G

Variant names:

• chr14-20437356-A-G
• rs1878705
• ENST00000800199.1:n.213-504A>G

Variant summary

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

The ENST00000800199.1(ENSG00000291038):​n.213-504A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.339 in 152,064 control chromosomes in the GnomAD database, including 9,034 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 0.34 (9034 hom., cov: 32)
• Consequence: ENSG00000291038 ENST00000800199.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.155
• Publications: 12 publications found

Genes affected

ENSG00000291038 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.375 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000291038	ENST00000800199.1	n.213-504A>G		intron_variant	Intron 1 of 7
ENSG00000291038	ENST00000800200.1	n.208-504A>G		intron_variant	Intron 1 of 6

Frequencies

GnomAD3 genomes AF: 0.339 AC: 51585 AN: 151946 Hom.: 9027 Cov.: 32

Gnomad AFR AF: 0.257

Gnomad AMI AF: 0.469

Gnomad AMR AF: 0.344

Gnomad ASJ AF: 0.359

Gnomad EAS AF: 0.319

Gnomad SAS AF: 0.373

Gnomad FIN AF: 0.380

Gnomad MID AF: 0.388

Gnomad NFE AF: 0.378

Gnomad OTH AF: 0.356

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

GnomAD4 genome AF: 0.339 AC: 51619 AN: 152064 Hom.: 9034 Cov.: 32 AF XY: 0.341 AC XY: 25312 AN XY: 74310

African (AFR) AF: 0.257 AC: 10642 AN: 41480

American (AMR) AF: 0.344 AC: 5252 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.359 AC: 1245 AN: 3468

East Asian (EAS) AF: 0.319 AC: 1645 AN: 5164

South Asian (SAS) AF: 0.375 AC: 1807 AN: 4824

European-Finnish (FIN) AF: 0.380 AC: 4017 AN: 10584

Middle Eastern (MID) AF: 0.386 AC: 112 AN: 290

European-Non Finnish (NFE) AF: 0.378 AC: 25717 AN: 67956

Other (OTH) AF: 0.358 AC: 754 AN: 2108

Alfa AF: 0.369 Hom.: 21342

Bravo AF: 0.332

Asia WGS AF: 0.339 AC: 1181 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.1
DANN	Benign	0.54
PhyloP100		0.15

Splicing

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

Other links and lift over

dbSNP: rs1878705; hg19: chr14-20905515; COSMIC: COSV60727879;