rs10483336

Positions:

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

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000548280.1(ENSG00000257869):​n.393-37042G>A variant causes a intron, non coding transcript 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: ENST00000548280.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.43

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000548280.1	n.393-37042G>A		intron_variant, non_coding_transcript_variant		4

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

Gnomad4 AFR AF: 0.0516

Gnomad4 AMR AF: 0.285

Gnomad4 ASJ AF: 0.204

Gnomad4 EAS AF: 0.0491

Gnomad4 SAS AF: 0.139

Gnomad4 FIN AF: 0.166

Gnomad4 NFE AF: 0.189

Gnomad4 OTH AF: 0.170

Alfa AF: 0.184 Hom.: 5966

Bravo AF: 0.156

Asia WGS AF: 0.115 AC: 401 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10483336; hg19: chr14-28837590;