rs17658378

Variant names:

• chr8-115381846-A-G
• rs17658378
• ENST00000748853.1:n.436-9126A>G

Variant summary

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

The ENST00000748853.1(ENSG00000297548):​n.436-9126A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0824 in 152,174 control chromosomes in the GnomAD database, including 759 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 0.082 (759 hom., cov: 31)
• Consequence: ENSG00000297548 ENST00000748853.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.347
• Publications: 5 publications found

Genes affected

ENSG00000297548 (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 (AMR) allele frequency at 95% confidence interval = 0.122 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
ENSG00000297548	ENST00000748853.1	n.436-9126A>G		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.0825 AC: 12541 AN: 152056 Hom.: 760 Cov.: 31

Gnomad AFR AF: 0.0244

Gnomad AMI AF: 0.223

Gnomad AMR AF: 0.126

Gnomad ASJ AF: 0.142

Gnomad EAS AF: 0.000773

Gnomad SAS AF: 0.0389

Gnomad FIN AF: 0.0418

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.117

Gnomad OTH AF: 0.117

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

GnomAD4 genome AF: 0.0824 AC: 12540 AN: 152174 Hom.: 759 Cov.: 31 AF XY: 0.0788 AC XY: 5859 AN XY: 74392

African (AFR) AF: 0.0243 AC: 1009 AN: 41512

American (AMR) AF: 0.126 AC: 1933 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.142 AC: 494 AN: 3468

East Asian (EAS) AF: 0.000775 AC: 4 AN: 5162

South Asian (SAS) AF: 0.0394 AC: 190 AN: 4824

European-Finnish (FIN) AF: 0.0418 AC: 444 AN: 10612

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.117 AC: 7972 AN: 67992

Other (OTH) AF: 0.116 AC: 245 AN: 2114

Alfa AF: 0.108 Hom.: 2772

Bravo AF: 0.0878

Asia WGS AF: 0.0180 AC: 63 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	3.2
DANN	Benign	0.75
PhyloP100		0.35

Splicing

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

Other links and lift over

dbSNP: rs17658378; hg19: chr8-116394075;