rs2867840

chr3-150153372-G-Achr3-150153372-G-C

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, non coding transcript 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: ENST00000487840.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.365

Genes affected

(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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000487840.5	n.139+28342G>A		intron_variant, non_coding_transcript_variant		2
	ENST00000489690.1	n.212+28342G>A		intron_variant, non_coding_transcript_variant		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;