14-54333321-T-C

Variant names:

• chr14-54333321-T-C
• rs10483634
• ENST00000770016.1:n.370-33144A>G

Variant summary

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

The ENST00000770016.1(ENSG00000300202):​n.370-33144A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.128 in 152,202 control chromosomes in the GnomAD database, including 1,637 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 0.13 (1637 hom., cov: 32)
• Consequence: ENSG00000300202 ENST00000770016.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0910
• Publications: 5 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=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.227 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000770016.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000300202	ENST00000770016.1		n.370-33144A>G		intron	N/A
	ENSG00000300202	ENST00000770017.1		n.410-33144A>G		intron	N/A
	ENSG00000300202	ENST00000770018.1		n.522-33144A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.128 AC: 19448 AN: 152084 Hom.: 1637 Cov.: 32

Gnomad AFR AF: 0.0299

Gnomad AMI AF: 0.151

Gnomad AMR AF: 0.191

Gnomad ASJ AF: 0.104

Gnomad EAS AF: 0.0756

Gnomad SAS AF: 0.237

Gnomad FIN AF: 0.243

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.153

Gnomad OTH AF: 0.128

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

GnomAD4 genome AF: 0.128 AC: 19445 AN: 152202 Hom.: 1637 Cov.: 32 AF XY: 0.136 AC XY: 10140 AN XY: 74394

African (AFR) AF: 0.0299 AC: 1241 AN: 41554

American (AMR) AF: 0.191 AC: 2920 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.104 AC: 362 AN: 3470

East Asian (EAS) AF: 0.0754 AC: 391 AN: 5188

South Asian (SAS) AF: 0.238 AC: 1148 AN: 4824

European-Finnish (FIN) AF: 0.243 AC: 2571 AN: 10586

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.153 AC: 10372 AN: 67994

Other (OTH) AF: 0.126 AC: 267 AN: 2114

Alfa AF: 0.151 Hom.: 1514

Bravo AF: 0.120

Asia WGS AF: 0.124 AC: 431 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.7
DANN	Benign	0.68
PhyloP100		-0.091

Splicing

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

Other links and lift over

dbSNP: rs10483634; hg19: chr14-54800039;