chr17-27804300-G-A

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 18 publications found

Genes affected

ENSG00000266202 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

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.261C>T	p.Cys87Cys	synonymous	Exon 4 of 5	ENSP00000462879.1	J3KTA2

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

GnomAD2 exomes AF: 0.300 AC: 3 AN: 10 AF XY: 0.500

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

African (AFR) AF: 0.146 AC: 1052 AN: 7184

American (AMR) AF: 0.0977 AC: 727 AN: 7438

Ashkenazi Jewish (ASJ) AF: 0.228 AC: 2103 AN: 9242

East Asian (EAS) AF: 0.0494 AC: 1132 AN: 22902

South Asian (SAS) AF: 0.136 AC: 413 AN: 3030

European-Finnish (FIN) AF: 0.163 AC: 3396 AN: 20824

Middle Eastern (MID) AF: 0.177 AC: 230 AN: 1300

European-Non Finnish (NFE) AF: 0.174 AC: 27479 AN: 158190

Other (OTH) AF: 0.160 AC: 2623 AN: 16376

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

African (AFR) AF: 0.142 AC: 5885 AN: 41554

American (AMR) AF: 0.120 AC: 1830 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.235 AC: 814 AN: 3468

East Asian (EAS) AF: 0.0500 AC: 259 AN: 5184

South Asian (SAS) AF: 0.141 AC: 681 AN: 4828

European-Finnish (FIN) AF: 0.166 AC: 1761 AN: 10604

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.169 AC: 11498 AN: 67986

Other (OTH) AF: 0.165 AC: 349 AN: 2114

Alfa AF: 0.163 Hom.: 4204

Bravo AF: 0.152

Asia WGS AF: 0.0810 AC: 281 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.026
DANN	Benign	0.80
PhyloP100		-1.8

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

Other links and lift over

dbSNP: rs2779251; hg19: chr17-26131326;