rs2779248

Variant names:

• chr17-27800806-T-C
• rs2779248
• ENST00000582441.1:c.439-1924A>G

Variant summary

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

The ENST00000582441.1(ENSG00000266202):​c.439-1924A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.388 in 151,956 control chromosomes in the GnomAD database, including 11,800 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 0.39 (11800 hom., cov: 31)
• Consequence: ENSG00000266202 ENST00000582441.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.58

Genes affected

ENSG00000266202 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.44 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
ENSG00000266202	ENST00000582441.1	c.439-1924A>G		intron_variant	Intron 4 of 4	4		ENSP00000462879.1

Frequencies

GnomAD3 genomes AF: 0.387 AC: 58834 AN: 151838 Hom.: 11793 Cov.: 31

Gnomad AFR AF: 0.445

Gnomad AMI AF: 0.583

Gnomad AMR AF: 0.346

Gnomad ASJ AF: 0.538

Gnomad EAS AF: 0.168

Gnomad SAS AF: 0.304

Gnomad FIN AF: 0.328

Gnomad MID AF: 0.570

Gnomad NFE AF: 0.382

Gnomad OTH AF: 0.405

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

GnomAD4 genome AF: 0.388 AC: 58888 AN: 151956 Hom.: 11800 Cov.: 31 AF XY: 0.382 AC XY: 28385 AN XY: 74278

Gnomad4 AFR AF: 0.445

Gnomad4 AMR AF: 0.347

Gnomad4 ASJ AF: 0.538

Gnomad4 EAS AF: 0.168

Gnomad4 SAS AF: 0.304

Gnomad4 FIN AF: 0.328

Gnomad4 NFE AF: 0.382

Gnomad4 OTH AF: 0.404

Alfa AF: 0.387 Hom.: 18782

Bravo AF: 0.396

Asia WGS AF: 0.230 AC: 798 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.044
DANN	Benign	0.56

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs2779248; hg19: chr17-26127832;