17-40514261-A-G

Variant names:

• chr17-40514261-A-G
• rs17708087
• ENST00000835260.1:n.128-756T>C

Variant summary

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

The ENST00000835260.1(ENSG00000308596):​n.128-756T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.146 in 151,952 control chromosomes in the GnomAD database, including 2,048 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 (2048 hom., cov: 30)
• Consequence: ENSG00000308596 ENST00000835260.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.837
• Publications: 5 publications found

Genes affected

ENSG00000308596 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.213 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
ENSG00000308596	ENST00000835260.1	n.128-756T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.146 AC: 22124 AN: 151832 Hom.: 2048 Cov.: 30

Gnomad AFR AF: 0.0398

Gnomad AMI AF: 0.311

Gnomad AMR AF: 0.113

Gnomad ASJ AF: 0.131

Gnomad EAS AF: 0.0786

Gnomad SAS AF: 0.141

Gnomad FIN AF: 0.183

Gnomad MID AF: 0.121

Gnomad NFE AF: 0.216

Gnomad OTH AF: 0.145

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

GnomAD4 genome AF: 0.146 AC: 22123 AN: 151952 Hom.: 2048 Cov.: 30 AF XY: 0.143 AC XY: 10631 AN XY: 74260

African (AFR) AF: 0.0397 AC: 1648 AN: 41478

American (AMR) AF: 0.113 AC: 1731 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.131 AC: 453 AN: 3470

East Asian (EAS) AF: 0.0786 AC: 401 AN: 5104

South Asian (SAS) AF: 0.141 AC: 678 AN: 4804

European-Finnish (FIN) AF: 0.183 AC: 1933 AN: 10570

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.216 AC: 14657 AN: 67932

Other (OTH) AF: 0.143 AC: 303 AN: 2114

Alfa AF: 0.181 Hom.: 4205

Bravo AF: 0.135

Asia WGS AF: 0.100 AC: 348 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	3.8
DANN	Benign	0.75
PhyloP100		0.84

Splicing

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

Other links and lift over

dbSNP: rs17708087; hg19: chr17-38670513;