rs2779249

Variant names:

• chr17-27801555-C-A
• rs2779249
• ENST00000582441.1:c.438+2568G>T

Variant summary

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

The ENST00000582441.1(ENSG00000266202):​c.438+2568G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.325 in 152,090 control chromosomes in the GnomAD database, including 8,568 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 0.32 (8568 hom., cov: 32)
• Consequence: ENSG00000266202 ENST00000582441.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.21
• Publications: 58 publications found

Genes affected

ENSG00000266202 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.424 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000582441.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000266202	ENST00000582441.1	TSL:4	c.438+2568G>T		intron	N/A	ENSP00000462879.1	J3KTA2

Frequencies

GnomAD3 genomes AF: 0.325 AC: 49315 AN: 151972 Hom.: 8561 Cov.: 32

Gnomad AFR AF: 0.429

Gnomad AMI AF: 0.471

Gnomad AMR AF: 0.266

Gnomad ASJ AF: 0.425

Gnomad EAS AF: 0.0612

Gnomad SAS AF: 0.243

Gnomad FIN AF: 0.251

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.303

Gnomad OTH AF: 0.332

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

GnomAD4 genome AF: 0.325 AC: 49372 AN: 152090 Hom.: 8568 Cov.: 32 AF XY: 0.319 AC XY: 23676 AN XY: 74328

African (AFR) AF: 0.429 AC: 17802 AN: 41458

American (AMR) AF: 0.266 AC: 4072 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.425 AC: 1475 AN: 3470

East Asian (EAS) AF: 0.0615 AC: 319 AN: 5188

South Asian (SAS) AF: 0.244 AC: 1174 AN: 4818

European-Finnish (FIN) AF: 0.251 AC: 2650 AN: 10570

Middle Eastern (MID) AF: 0.435 AC: 127 AN: 292

European-Non Finnish (NFE) AF: 0.303 AC: 20625 AN: 67984

Other (OTH) AF: 0.330 AC: 699 AN: 2116

Alfa AF: 0.314 Hom.: 10184

Bravo AF: 0.334

Asia WGS AF: 0.167 AC: 581 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.17
DANN	Benign	0.37
PhyloP100		-1.2

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2779249;

hg19: chr17-26128581;