rs2844559

Variant names:

• chr6-31372298-C-T
• rs2844559
• ENST00000649421.2:n.275-2585C>T

Variant summary

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

The ENST00000649421.2(ENSG00000285647):​n.275-2585C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0798 in 151,242 control chromosomes in the GnomAD database, including 808 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 0.080 (808 hom., cov: 32)
• Consequence: ENSG00000285647 ENST00000649421.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.295
• Publications: 22 publications found

Genes affected

ENSG00000285647 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.119 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	ENST00000649421.2	n.275-2585C>T		intron_variant	Intron 1 of 1
ENSG00000298426	ENST00000755446.1	n.327-9682C>T		intron_variant	Intron 1 of 1
ENSG00000285647	ENST00000755530.1	n.203-2585C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0798 AC: 12061 AN: 151130 Hom.: 808 Cov.: 32

Gnomad AFR AF: 0.0373

Gnomad AMI AF: 0.152

Gnomad AMR AF: 0.0413

Gnomad ASJ AF: 0.0462

Gnomad EAS AF: 0.00489

Gnomad SAS AF: 0.0685

Gnomad FIN AF: 0.0884

Gnomad MID AF: 0.0382

Gnomad NFE AF: 0.121

Gnomad OTH AF: 0.0629

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

GnomAD4 genome AF: 0.0798 AC: 12065 AN: 151242 Hom.: 808 Cov.: 32 AF XY: 0.0756 AC XY: 5581 AN XY: 73784

African (AFR) AF: 0.0373 AC: 1545 AN: 41458

American (AMR) AF: 0.0412 AC: 616 AN: 14936

Ashkenazi Jewish (ASJ) AF: 0.0462 AC: 160 AN: 3464

East Asian (EAS) AF: 0.00470 AC: 24 AN: 5102

South Asian (SAS) AF: 0.0696 AC: 323 AN: 4638

European-Finnish (FIN) AF: 0.0884 AC: 926 AN: 10478

Middle Eastern (MID) AF: 0.0377 AC: 11 AN: 292

European-Non Finnish (NFE) AF: 0.121 AC: 8191 AN: 67858

Other (OTH) AF: 0.0622 AC: 131 AN: 2106

Alfa AF: 0.0996 Hom.: 2044

Bravo AF: 0.0731

Asia WGS AF: 0.0230 AC: 80 AN: 3404

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	9.7
DANN	Benign	0.65
PhyloP100		-0.29

Splicing

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

Other links and lift over

dbSNP: rs2844559; hg19: chr6-31340075;