ENST00000553947.1:n.*667+2685G>A

Variant names:

• chr14-94600896-G-A
• rs4375593
• ENST00000553947.1:n.*667+2685G>A

Variant summary

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

The ENST00000553947.1(ENSG00000273259):​n.*667+2685G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.385 in 151,570 control chromosomes in the GnomAD database, including 12,407 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 (12407 hom., cov: 31)
• Consequence: ENSG00000273259 ENST00000553947.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.841
• Publications: 1 publications found

Genes affected

ENSG00000273259 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.577 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
ENSG00000273259	ENST00000553947.1	n.*667+2685G>A		intron_variant	Intron 3 of 7	2		ENSP00000452367.2
ENSG00000288028	ENST00000656621.1	n.70+1367G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.385 AC: 58318 AN: 151452 Hom.: 12381 Cov.: 31

Gnomad AFR AF: 0.583

Gnomad AMI AF: 0.231

Gnomad AMR AF: 0.277

Gnomad ASJ AF: 0.327

Gnomad EAS AF: 0.372

Gnomad SAS AF: 0.308

Gnomad FIN AF: 0.317

Gnomad MID AF: 0.379

Gnomad NFE AF: 0.312

Gnomad OTH AF: 0.370

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

GnomAD4 genome AF: 0.385 AC: 58386 AN: 151570 Hom.: 12407 Cov.: 31 AF XY: 0.380 AC XY: 28116 AN XY: 74080

African (AFR) AF: 0.583 AC: 24017 AN: 41202

American (AMR) AF: 0.277 AC: 4220 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.327 AC: 1133 AN: 3460

East Asian (EAS) AF: 0.372 AC: 1904 AN: 5112

South Asian (SAS) AF: 0.308 AC: 1480 AN: 4808

European-Finnish (FIN) AF: 0.317 AC: 3333 AN: 10520

Middle Eastern (MID) AF: 0.387 AC: 113 AN: 292

European-Non Finnish (NFE) AF: 0.312 AC: 21207 AN: 67902

Other (OTH) AF: 0.365 AC: 769 AN: 2108

Alfa AF: 0.365 Hom.: 1378

Bravo AF: 0.391

Asia WGS AF: 0.341 AC: 1185 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.23
DANN	Benign	0.41
PhyloP100		-0.84

Splicing

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

Other links and lift over

dbSNP: rs4375593; hg19: chr14-95067233;