17-70315539-C-T

Variant names:

• chr17-70315539-C-T
• rs312736
• ENST00000592809.1:n.177-2151G>A

Variant summary

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

The ENST00000592809.1(ENSG00000267109):​n.177-2151G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.45 in 151,896 control chromosomes in the GnomAD database, including 15,466 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 0.45 (15466 hom., cov: 31)
• Consequence: ENSG00000267109 ENST00000592809.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.27
• Publications: 4 publications found

Genes affected

ENSG00000267109 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.465 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
ENSG00000267109	ENST00000592809.1	n.177-2151G>A		intron_variant	Intron 2 of 2	3

Frequencies

GnomAD3 genomes AF: 0.450 AC: 68309 AN: 151780 Hom.: 15447 Cov.: 31

Gnomad AFR AF: 0.447

Gnomad AMI AF: 0.554

Gnomad AMR AF: 0.449

Gnomad ASJ AF: 0.439

Gnomad EAS AF: 0.479

Gnomad SAS AF: 0.469

Gnomad FIN AF: 0.374

Gnomad MID AF: 0.538

Gnomad NFE AF: 0.459

Gnomad OTH AF: 0.438

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

GnomAD4 genome AF: 0.450 AC: 68358 AN: 151896 Hom.: 15466 Cov.: 31 AF XY: 0.447 AC XY: 33178 AN XY: 74204

African (AFR) AF: 0.447 AC: 18519 AN: 41414

American (AMR) AF: 0.450 AC: 6867 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.439 AC: 1524 AN: 3468

East Asian (EAS) AF: 0.481 AC: 2476 AN: 5152

South Asian (SAS) AF: 0.468 AC: 2253 AN: 4814

European-Finnish (FIN) AF: 0.374 AC: 3935 AN: 10528

Middle Eastern (MID) AF: 0.537 AC: 158 AN: 294

European-Non Finnish (NFE) AF: 0.459 AC: 31201 AN: 67936

Other (OTH) AF: 0.436 AC: 921 AN: 2112

Alfa AF: 0.449 Hom.: 1969

Bravo AF: 0.456

Asia WGS AF: 0.468 AC: 1624 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.27
DANN	Benign	0.60
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs312736; hg19: chr17-68311680;