rs10483336

Variant names:

• chr14-28368384-G-A
• rs10483336
• ENST00000548280.1:n.393-37042G>A

Your query was ambiguous. Multiple possible variants found:

• chr14-28368384-G-A
• chr14-28368384-G-C
• chr14-28368384-G-T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000548280.1(ENSG00000257869):​n.393-37042G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.153 in 151,760 control chromosomes in the GnomAD database, including 2,265 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 0.15 (2265 hom., cov: 32)
• Consequence: ENSG00000257869 ENST00000548280.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.43
• Publications: 4 publications found

Genes affected

ENSG00000257869 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.38).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.278 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000548280.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000257869	ENST00000548280.1	TSL:4	n.393-37042G>A		intron	N/A
	ENSG00000257869	ENST00000745978.1		n.310-37042G>A		intron	N/A
	ENSG00000257869	ENST00000745979.1		n.139-37042G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.153 AC: 23173 AN: 151642 Hom.: 2255 Cov.: 32

Gnomad AFR AF: 0.0516

Gnomad AMI AF: 0.145

Gnomad AMR AF: 0.284

Gnomad ASJ AF: 0.204

Gnomad EAS AF: 0.0488

Gnomad SAS AF: 0.139

Gnomad FIN AF: 0.166

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.189

Gnomad OTH AF: 0.170

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

GnomAD4 genome AF: 0.153 AC: 23204 AN: 151760 Hom.: 2265 Cov.: 32 AF XY: 0.154 AC XY: 11421 AN XY: 74180

African (AFR) AF: 0.0516 AC: 2142 AN: 41488

American (AMR) AF: 0.285 AC: 4333 AN: 15214

Ashkenazi Jewish (ASJ) AF: 0.204 AC: 706 AN: 3466

East Asian (EAS) AF: 0.0491 AC: 254 AN: 5172

South Asian (SAS) AF: 0.139 AC: 669 AN: 4816

European-Finnish (FIN) AF: 0.166 AC: 1755 AN: 10582

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.189 AC: 12789 AN: 67706

Other (OTH) AF: 0.170 AC: 358 AN: 2110

Alfa AF: 0.180 Hom.: 12247

Bravo AF: 0.156

Asia WGS AF: 0.115 AC: 401 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.38
CADD	Benign	14
DANN	Benign	0.50
PhyloP100		2.4

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10483336;

hg19: chr14-28837590;