ENST00000487840.5:n.139+28342G>A

Variant names:

• chr3-150153372-G-A
• rs2867840
• ENST00000487840.5:n.139+28342G>A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000487840.5(ENSG00000243944):​n.139+28342G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.201 in 152,074 control chromosomes in the GnomAD database, including 3,201 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 0.20 (3201 hom., cov: 32)
• Consequence: ENSG00000243944 ENST00000487840.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.365

Genes affected

ENSG00000243944 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.261 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000243944	ENST00000487840.5	n.139+28342G>A		intron_variant	Intron 2 of 2	2
ENSG00000243944	ENST00000489690.1	n.212+28342G>A		intron_variant	Intron 2 of 2	3

Frequencies

GnomAD3 genomes AF: 0.201 AC: 30614 AN: 151958 Hom.: 3202 Cov.: 32

Gnomad AFR AF: 0.153

Gnomad AMI AF: 0.236

Gnomad AMR AF: 0.212

Gnomad ASJ AF: 0.207

Gnomad EAS AF: 0.144

Gnomad SAS AF: 0.272

Gnomad FIN AF: 0.163

Gnomad MID AF: 0.303

Gnomad NFE AF: 0.233

Gnomad OTH AF: 0.207

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

GnomAD4 genome AF: 0.201 AC: 30624 AN: 152074 Hom.: 3201 Cov.: 32 AF XY: 0.199 AC XY: 14769 AN XY: 74336

Gnomad4 AFR AF: 0.153

Gnomad4 AMR AF: 0.212

Gnomad4 ASJ AF: 0.207

Gnomad4 EAS AF: 0.145

Gnomad4 SAS AF: 0.273

Gnomad4 FIN AF: 0.163

Gnomad4 NFE AF: 0.233

Gnomad4 OTH AF: 0.206

Alfa AF: 0.221 Hom.: 4861

Bravo AF: 0.201

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	13
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2867840; hg19: chr3-149871159;