chr14-54381173-C-G

Variant names:

• chr14-54381173-C-G
• rs2143956
• ENST00000770016.1:n.369+6915G>C

Variant summary

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

The ENST00000770016.1(ENSG00000300202):​n.369+6915G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.496 in 151,866 control chromosomes in the GnomAD database, including 19,641 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 0.50 (19641 hom., cov: 31)
• Consequence: ENSG00000300202 ENST00000770016.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.798
• Publications: 4 publications found

Genes affected

ENSG00000300202 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.583 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
ENSG00000300202	ENST00000770016.1	n.369+6915G>C		intron_variant	Intron 3 of 3
ENSG00000300202	ENST00000770017.1	n.409+6915G>C		intron_variant	Intron 2 of 2
ENSG00000300202	ENST00000770018.1	n.403-4414G>C		intron_variant	Intron 2 of 3
ENSG00000300202	ENST00000770019.1	n.403-2987G>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.496 AC: 75330 AN: 151748 Hom.: 19627 Cov.: 31

Gnomad AFR AF: 0.345

Gnomad AMI AF: 0.599

Gnomad AMR AF: 0.526

Gnomad ASJ AF: 0.619

Gnomad EAS AF: 0.275

Gnomad SAS AF: 0.394

Gnomad FIN AF: 0.552

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.588

Gnomad OTH AF: 0.543

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

GnomAD4 genome AF: 0.496 AC: 75380 AN: 151866 Hom.: 19641 Cov.: 31 AF XY: 0.493 AC XY: 36568 AN XY: 74164

African (AFR) AF: 0.345 AC: 14290 AN: 41378

American (AMR) AF: 0.526 AC: 8032 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.619 AC: 2147 AN: 3466

East Asian (EAS) AF: 0.275 AC: 1414 AN: 5142

South Asian (SAS) AF: 0.394 AC: 1895 AN: 4804

European-Finnish (FIN) AF: 0.552 AC: 5813 AN: 10526

Middle Eastern (MID) AF: 0.469 AC: 138 AN: 294

European-Non Finnish (NFE) AF: 0.588 AC: 39977 AN: 67970

Other (OTH) AF: 0.538 AC: 1131 AN: 2104

Alfa AF: 0.412 Hom.: 1243

Bravo AF: 0.489

Asia WGS AF: 0.339 AC: 1182 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.36
DANN	Benign	0.19
PhyloP100		-0.80

Splicing

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

Other links and lift over

dbSNP: rs2143956; hg19: chr14-54847891;