rs2844559

Positions:

• chr6-31372298-C-T

Variant summary

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

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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.295

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
		n.31372298C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000285647	ENST00000649421.1	n.275-2585C>T		intron_variant

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

Gnomad4 AFR AF: 0.0373

Gnomad4 AMR AF: 0.0412

Gnomad4 ASJ AF: 0.0462

Gnomad4 EAS AF: 0.00470

Gnomad4 SAS AF: 0.0696

Gnomad4 FIN AF: 0.0884

Gnomad4 NFE AF: 0.121

Gnomad4 OTH AF: 0.0622

Alfa AF: 0.110 Hom.: 1368

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2844559; hg19: chr6-31340075;