17-61617277-T-C

Variant names:

• chr17-61617277-T-C
• rs2040609
• ENST00000849359.1:n.172+25922T>C

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000849359.1(ENSG00000310374):​n.172+25922T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.3 in 152,122 control chromosomes in the GnomAD database, including 7,073 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 0.30 (7073 hom., cov: 32)
• Consequence: ENSG00000310374 ENST00000849359.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.37
• Publications: 4 publications found

Genes affected

ENSG00000310374 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.3).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.485 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
ENSG00000310374	ENST00000849359.1	n.172+25922T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.300 AC: 45655 AN: 152004 Hom.: 7062 Cov.: 32

Gnomad AFR AF: 0.308

Gnomad AMI AF: 0.253

Gnomad AMR AF: 0.301

Gnomad ASJ AF: 0.261

Gnomad EAS AF: 0.500

Gnomad SAS AF: 0.248

Gnomad FIN AF: 0.218

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.299

Gnomad OTH AF: 0.308

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

GnomAD4 genome AF: 0.300 AC: 45699 AN: 152122 Hom.: 7073 Cov.: 32 AF XY: 0.298 AC XY: 22200 AN XY: 74382

African (AFR) AF: 0.308 AC: 12783 AN: 41488

American (AMR) AF: 0.300 AC: 4596 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.261 AC: 905 AN: 3468

East Asian (EAS) AF: 0.501 AC: 2589 AN: 5172

South Asian (SAS) AF: 0.248 AC: 1195 AN: 4820

European-Finnish (FIN) AF: 0.218 AC: 2312 AN: 10584

Middle Eastern (MID) AF: 0.350 AC: 103 AN: 294

European-Non Finnish (NFE) AF: 0.299 AC: 20330 AN: 67982

Other (OTH) AF: 0.311 AC: 657 AN: 2112

Alfa AF: 0.292 Hom.: 1353

Bravo AF: 0.307

Asia WGS AF: 0.330 AC: 1145 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.30
CADD	Benign	22
DANN	Benign	0.81
PhyloP100		2.4

Splicing

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

Other links and lift over

dbSNP: rs2040609; hg19: chr17-59694638;