rs284744

Variant names:

• chr5-35470186-T-G
• rs284744
• ENST00000824642.1:n.137-16517T>G

Variant summary

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

The ENST00000824642.1(ENSG00000307231):​n.137-16517T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.327 in 152,206 control chromosomes in the GnomAD database, including 10,462 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 0.33 (10462 hom., cov: 33)
• Consequence: ENSG00000307231 ENST00000824642.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.161
• Publications: 1 publications found

Genes affected

ENSG00000307231 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.566 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000824642.1. 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
	ENSG00000307231	ENST00000824642.1		n.137-16517T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.326 AC: 49640 AN: 152088 Hom.: 10412 Cov.: 33

Gnomad AFR AF: 0.571

Gnomad AMI AF: 0.200

Gnomad AMR AF: 0.349

Gnomad ASJ AF: 0.168

Gnomad EAS AF: 0.488

Gnomad SAS AF: 0.379

Gnomad FIN AF: 0.153

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.194

Gnomad OTH AF: 0.302

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

GnomAD4 genome AF: 0.327 AC: 49753 AN: 152206 Hom.: 10462 Cov.: 33 AF XY: 0.328 AC XY: 24389 AN XY: 74430

African (AFR) AF: 0.572 AC: 23744 AN: 41498

American (AMR) AF: 0.350 AC: 5347 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.168 AC: 583 AN: 3472

East Asian (EAS) AF: 0.488 AC: 2524 AN: 5172

South Asian (SAS) AF: 0.378 AC: 1825 AN: 4830

European-Finnish (FIN) AF: 0.153 AC: 1628 AN: 10608

Middle Eastern (MID) AF: 0.269 AC: 79 AN: 294

European-Non Finnish (NFE) AF: 0.194 AC: 13191 AN: 68018

Other (OTH) AF: 0.307 AC: 650 AN: 2114

Alfa AF: 0.253 Hom.: 1240

Bravo AF: 0.352

Asia WGS AF: 0.436 AC: 1518 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	5.1
DANN	Benign	0.74
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs284744; hg19: chr5-35470288;