rs17412740

Variant names:

• chr8-20389247-G-A
• rs17412740
• ENST00000822544.1:n.301+29467G>A

Variant summary

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

The ENST00000822544.1(ENSG00000253164):​n.301+29467G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0486 in 152,244 control chromosomes in the GnomAD database, including 246 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 0.049 (246 hom., cov: 32)
• Consequence: ENSG00000253164 ENST00000822544.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.43
• Publications: 9 publications found

Genes affected

ENSG00000253164 (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 = 0.0818 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
ENSG00000253164	ENST00000822544.1	n.301+29467G>A		intron_variant	Intron 2 of 2
ENSG00000253164	ENST00000822545.1	n.445+29467G>A		intron_variant	Intron 3 of 3
ENSG00000253164	ENST00000822546.1	n.422+16522G>A		intron_variant	Intron 3 of 6

Frequencies

GnomAD3 genomes AF: 0.0486 AC: 7392 AN: 152126 Hom.: 244 Cov.: 32

Gnomad AFR AF: 0.0128

Gnomad AMI AF: 0.0230

Gnomad AMR AF: 0.0355

Gnomad ASJ AF: 0.0928

Gnomad EAS AF: 0.0885

Gnomad SAS AF: 0.0760

Gnomad FIN AF: 0.0409

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0676

Gnomad OTH AF: 0.0464

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

GnomAD4 genome AF: 0.0486 AC: 7400 AN: 152244 Hom.: 246 Cov.: 32 AF XY: 0.0476 AC XY: 3547 AN XY: 74454

African (AFR) AF: 0.0128 AC: 532 AN: 41550

American (AMR) AF: 0.0354 AC: 541 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0928 AC: 322 AN: 3470

East Asian (EAS) AF: 0.0885 AC: 458 AN: 5176

South Asian (SAS) AF: 0.0769 AC: 371 AN: 4822

European-Finnish (FIN) AF: 0.0409 AC: 434 AN: 10604

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.0676 AC: 4599 AN: 68016

Other (OTH) AF: 0.0497 AC: 105 AN: 2112

Alfa AF: 0.0595 Hom.: 554

Bravo AF: 0.0477

Asia WGS AF: 0.0790 AC: 273 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	0.49
DANN	Benign	0.56
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs17412740; hg19: chr8-20246758;