chr14-54390568-G-A

Variant names:

• chr14-54390568-G-A
• rs4293296
• ENST00000770016.1:n.126-1634C>T

Variant summary

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

The ENST00000770016.1(ENSG00000300202):​n.126-1634C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.258 in 150,164 control chromosomes in the GnomAD database, including 5,152 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 0.26 (5152 hom., cov: 32)
• Consequence: ENSG00000300202 ENST00000770016.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.243
• Publications: 11 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=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.285 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.126-1634C>T		intron_variant	Intron 1 of 3
ENSG00000300202	ENST00000770017.1	n.252+1759C>T		intron_variant	Intron 1 of 2
ENSG00000300202	ENST00000770018.1	n.245+1759C>T		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.258 AC: 38723 AN: 150046 Hom.: 5144 Cov.: 32

Gnomad AFR AF: 0.289

Gnomad AMI AF: 0.437

Gnomad AMR AF: 0.265

Gnomad ASJ AF: 0.227

Gnomad EAS AF: 0.135

Gnomad SAS AF: 0.197

Gnomad FIN AF: 0.169

Gnomad MID AF: 0.293

Gnomad NFE AF: 0.264

Gnomad OTH AF: 0.235

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

GnomAD4 genome AF: 0.258 AC: 38758 AN: 150164 Hom.: 5152 Cov.: 32 AF XY: 0.254 AC XY: 18577 AN XY: 73160

African (AFR) AF: 0.290 AC: 11915 AN: 41132

American (AMR) AF: 0.265 AC: 3950 AN: 14896

Ashkenazi Jewish (ASJ) AF: 0.227 AC: 782 AN: 3442

East Asian (EAS) AF: 0.134 AC: 679 AN: 5070

South Asian (SAS) AF: 0.196 AC: 913 AN: 4666

European-Finnish (FIN) AF: 0.169 AC: 1715 AN: 10164

Middle Eastern (MID) AF: 0.305 AC: 89 AN: 292

European-Non Finnish (NFE) AF: 0.264 AC: 17839 AN: 67528

Other (OTH) AF: 0.232 AC: 479 AN: 2066

Alfa AF: 0.262 Hom.: 20473

Bravo AF: 0.263

Asia WGS AF: 0.165 AC: 573 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.9
DANN	Benign	0.80
PhyloP100		0.24

Splicing

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

Other links and lift over

dbSNP: rs4293296; hg19: chr14-54857286;