14-81950927-C-G

Variant names:

• chr14-81950927-C-G
• rs1953408
• ENST00000554814.1:n.316-79179C>G

Variant summary

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

The ENST00000554814.1(ENSG00000259035):​n.316-79179C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.388 in 151,870 control chromosomes in the GnomAD database, including 12,830 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 (12830 hom., cov: 31)
• Consequence: ENSG00000259035 ENST00000554814.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0780
• Publications: 2 publications found

Genes affected

ENSG00000259035 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.586 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107984704	XR_007064292.1	n.842-123001C>G		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000259035	ENST00000554814.1	n.316-79179C>G		intron_variant	Intron 3 of 3	4

Frequencies

GnomAD3 genomes AF: 0.387 AC: 58749 AN: 151754 Hom.: 12782 Cov.: 31

Gnomad AFR AF: 0.592

Gnomad AMI AF: 0.311

Gnomad AMR AF: 0.386

Gnomad ASJ AF: 0.273

Gnomad EAS AF: 0.382

Gnomad SAS AF: 0.405

Gnomad FIN AF: 0.322

Gnomad MID AF: 0.245

Gnomad NFE AF: 0.280

Gnomad OTH AF: 0.384

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

GnomAD4 genome AF: 0.388 AC: 58868 AN: 151870 Hom.: 12830 Cov.: 31 AF XY: 0.388 AC XY: 28770 AN XY: 74204

African (AFR) AF: 0.592 AC: 24530 AN: 41418

American (AMR) AF: 0.386 AC: 5897 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.273 AC: 948 AN: 3468

East Asian (EAS) AF: 0.382 AC: 1963 AN: 5134

South Asian (SAS) AF: 0.404 AC: 1945 AN: 4810

European-Finnish (FIN) AF: 0.322 AC: 3398 AN: 10538

Middle Eastern (MID) AF: 0.257 AC: 75 AN: 292

European-Non Finnish (NFE) AF: 0.280 AC: 19009 AN: 67932

Other (OTH) AF: 0.389 AC: 819 AN: 2108

Alfa AF: 0.333 Hom.: 1181

Bravo AF: 0.401

Asia WGS AF: 0.439 AC: 1525 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.81
DANN	Benign	0.63
PhyloP100		0.078

Splicing

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

Other links and lift over

dbSNP: rs1953408; hg19: chr14-82417271;