rs2779251

Variant names:

• chr17-27804300-G-A
• rs2779251
• ENST00000582441.1:c.261C>T

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_Strong BP7 BA1

The ENST00000582441.1(ENSG00000266202):​c.261C>T​(p.Cys87Cys) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.157 in 398,732 control chromosomes in the GnomAD database, including 5,273 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 0.15 (1920 hom., cov: 32)
  • Exomes 𝑓: 0.16 (3353 hom.)
• Consequence: ENSG00000266202 ENST00000582441.1 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.76

Genes affected

ENSG00000266202 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BP7: Synonymous conserved (PhyloP=-1.76 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.167 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.261C>T	p.Cys87Cys	synonymous_variant	Exon 4 of 5	4		ENSP00000462879.1

Frequencies

GnomAD3 genomes AF: 0.154 AC: 23418 AN: 152128 Hom.: 1921 Cov.: 32

Gnomad AFR AF: 0.142

Gnomad AMI AF: 0.333

Gnomad AMR AF: 0.120

Gnomad ASJ AF: 0.235

Gnomad EAS AF: 0.0498

Gnomad SAS AF: 0.141

Gnomad FIN AF: 0.166

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.169

Gnomad OTH AF: 0.168

GnomAD3 exomes AF: 0.300 AC: 3 AN: 10 Hom.: 0 AF XY: 0.500 AC XY: 1 AN XY: 2

Gnomad AFR exome AF: 0.00

Gnomad NFE exome AF: 0.375

GnomAD4 exome AF: 0.159 AC: 39155 AN: 246486 Hom.: 3353 Cov.: 0 AF XY: 0.160 AC XY: 19986 AN XY: 124942

Gnomad4 AFR exome AF: 0.146

Gnomad4 AMR exome AF: 0.0977

Gnomad4 ASJ exome AF: 0.228

Gnomad4 EAS exome AF: 0.0494

Gnomad4 SAS exome AF: 0.136

Gnomad4 FIN exome AF: 0.163

Gnomad4 NFE exome AF: 0.174

Gnomad4 OTH exome AF: 0.160

GnomAD4 genome AF: 0.154 AC: 23422 AN: 152246 Hom.: 1920 Cov.: 32 AF XY: 0.152 AC XY: 11323 AN XY: 74456

Gnomad4 AFR AF: 0.142

Gnomad4 AMR AF: 0.120

Gnomad4 ASJ AF: 0.235

Gnomad4 EAS AF: 0.0500

Gnomad4 SAS AF: 0.141

Gnomad4 FIN AF: 0.166

Gnomad4 NFE AF: 0.169

Gnomad4 OTH AF: 0.165

Alfa AF: 0.164 Hom.: 1021

Bravo AF: 0.152

Asia WGS AF: 0.0810 AC: 281 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.026
DANN	Benign	0.80

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: rs2779251; hg19: chr17-26131326;