chr14-94600900-T-C

Variant names:

• chr14-94600900-T-C
• rs4508366
• ENST00000553947.1:n.*667+2689T>C

Variant summary

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

The ENST00000553947.1(ENSG00000273259):​n.*667+2689T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.386 in 151,290 control chromosomes in the GnomAD database, including 12,412 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 (12412 hom., cov: 31)
• Consequence: ENSG00000273259 ENST00000553947.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.187
• 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.578 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000553947.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000273259	ENST00000553947.1	TSL:2	n.*667+2689T>C		intron	N/A	ENSP00000452367.2
	ENSG00000288028	ENST00000656621.1		n.70+1371T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.386 AC: 58325 AN: 151172 Hom.: 12386 Cov.: 31

Gnomad AFR AF: 0.583

Gnomad AMI AF: 0.231

Gnomad AMR AF: 0.278

Gnomad ASJ AF: 0.327

Gnomad EAS AF: 0.374

Gnomad SAS AF: 0.309

Gnomad FIN AF: 0.318

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.313

Gnomad OTH AF: 0.371

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

GnomAD4 genome AF: 0.386 AC: 58393 AN: 151290 Hom.: 12412 Cov.: 31 AF XY: 0.380 AC XY: 28103 AN XY: 73894

African (AFR) AF: 0.584 AC: 24028 AN: 41162

American (AMR) AF: 0.277 AC: 4221 AN: 15216

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

East Asian (EAS) AF: 0.374 AC: 1908 AN: 5096

South Asian (SAS) AF: 0.310 AC: 1482 AN: 4788

European-Finnish (FIN) AF: 0.318 AC: 3328 AN: 10460

Middle Eastern (MID) AF: 0.384 AC: 113 AN: 294

European-Non Finnish (NFE) AF: 0.313 AC: 21202 AN: 67806

Other (OTH) AF: 0.366 AC: 768 AN: 2100

Alfa AF: 0.365 Hom.: 1377

Bravo AF: 0.391

Asia WGS AF: 0.340 AC: 1184 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.4
DANN	Benign	0.57
PhyloP100		-0.19

Splicing

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

Other links and lift over

dbSNP: rs4508366; hg19: chr14-95067237;