rs2857654

Variant names:

• chr17-34252512-C-A
• rs2857654
• ENST00000776537.1:n.9G>T

Your query was ambiguous. Multiple possible variants found:

• chr17-34252512-C-A
• chr17-34252512-C-G
• chr17-34252512-C-T

Variant summary

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

The ENST00000776537.1(ENSG00000301139):​n.9G>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.334 in 152,076 control chromosomes in the GnomAD database, including 9,011 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 0.33 (9011 hom., cov: 33)
• Consequence: ENSG00000301139 ENST00000776537.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.365
• Publications: 15 publications found

Genes affected

ENSG00000301139 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.539 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
ENSG00000301139	ENST00000776537.1	n.9G>T		non_coding_transcript_exon_variant	Exon 1 of 3
ENSG00000301139	ENST00000776538.1	n.9G>T		non_coding_transcript_exon_variant	Exon 1 of 3
ENSG00000301139	ENST00000776539.1	n.7G>T		non_coding_transcript_exon_variant	Exon 1 of 3
ENSG00000301139	ENST00000776541.1	n.-5G>T		upstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.334 AC: 50752 AN: 151958 Hom.: 8991 Cov.: 33

Gnomad AFR AF: 0.366

Gnomad AMI AF: 0.140

Gnomad AMR AF: 0.450

Gnomad ASJ AF: 0.282

Gnomad EAS AF: 0.556

Gnomad SAS AF: 0.343

Gnomad FIN AF: 0.344

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.276

Gnomad OTH AF: 0.320

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

GnomAD4 genome AF: 0.334 AC: 50805 AN: 152076 Hom.: 9011 Cov.: 33 AF XY: 0.340 AC XY: 25312 AN XY: 74348

African (AFR) AF: 0.365 AC: 15152 AN: 41462

American (AMR) AF: 0.451 AC: 6899 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.282 AC: 979 AN: 3470

East Asian (EAS) AF: 0.556 AC: 2853 AN: 5130

South Asian (SAS) AF: 0.343 AC: 1655 AN: 4820

European-Finnish (FIN) AF: 0.344 AC: 3641 AN: 10580

Middle Eastern (MID) AF: 0.303 AC: 89 AN: 294

European-Non Finnish (NFE) AF: 0.276 AC: 18736 AN: 68002

Other (OTH) AF: 0.319 AC: 673 AN: 2112

Alfa AF: 0.217 Hom.: 660

Bravo AF: 0.344

Asia WGS AF: 0.452 AC: 1569 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	3.7
DANN	Benign	0.51
PhyloP100		0.36

Splicing

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

Other links and lift over

dbSNP: rs2857654; hg19: chr17-32579531;