rs2779251

Positions:

• chr17-27804300-G-A

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000266202	ENST00000582441.1	c.261C>T	p.Cys87Cys	synonymous_variant	4/5	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;