rs2394990

Variant names:

• chr6-31372782-C-A
• rs2394990
• ENST00000649421.1:n.275-2101C>A

Variant summary

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

The ENST00000649421.1(ENSG00000285647):​n.275-2101C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.568 in 150,458 control chromosomes in the GnomAD database, including 25,342 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 0.57 (25342 hom., cov: 30)
• Consequence: ENSG00000285647 ENST00000649421.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.580

Genes affected

ENSG00000285647 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.697 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
ENSG00000285647	ENST00000649421.1	n.275-2101C>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.569 AC: 85472 AN: 150344 Hom.: 25324 Cov.: 30

Gnomad AFR AF: 0.501

Gnomad AMI AF: 0.584

Gnomad AMR AF: 0.515

Gnomad ASJ AF: 0.413

Gnomad EAS AF: 0.717

Gnomad SAS AF: 0.657

Gnomad FIN AF: 0.509

Gnomad MID AF: 0.600

Gnomad NFE AF: 0.620

Gnomad OTH AF: 0.585

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

GnomAD4 genome AF: 0.568 AC: 85525 AN: 150458 Hom.: 25342 Cov.: 30 AF XY: 0.566 AC XY: 41462 AN XY: 73280

Gnomad4 AFR AF: 0.501

Gnomad4 AMR AF: 0.515

Gnomad4 ASJ AF: 0.413

Gnomad4 EAS AF: 0.717

Gnomad4 SAS AF: 0.658

Gnomad4 FIN AF: 0.509

Gnomad4 NFE AF: 0.620

Gnomad4 OTH AF: 0.590

Alfa AF: 0.602 Hom.: 13558

Bravo AF: 0.564

Asia WGS AF: 0.641 AC: 2182 AN: 3404

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.2
DANN	Benign	0.16

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2394990; hg19: chr6-31340559;