rs9353527

Variant names:

• chr6-88170320-G-A
• rs9353527
• ENST00000756364.1:n.129-41277G>A

Variant summary

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

The ENST00000756364.1(ENSG00000298549):​n.129-41277G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.603 in 151,764 control chromosomes in the GnomAD database, including 28,339 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 0.60 (28339 hom., cov: 30)
• Consequence: ENSG00000298549 ENST00000756364.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.172
• Publications: 3 publications found

Genes affected

ENSG00000298549 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.756 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
ENSG00000298549	ENST00000756364.1	n.129-41277G>A		intron_variant	Intron 1 of 2
ENSG00000298549	ENST00000756365.1	n.571+51G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.603 AC: 91497 AN: 151648 Hom.: 28328 Cov.: 30

Gnomad AFR AF: 0.447

Gnomad AMI AF: 0.738

Gnomad AMR AF: 0.588

Gnomad ASJ AF: 0.610

Gnomad EAS AF: 0.775

Gnomad SAS AF: 0.621

Gnomad FIN AF: 0.628

Gnomad MID AF: 0.706

Gnomad NFE AF: 0.680

Gnomad OTH AF: 0.634

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

GnomAD4 genome AF: 0.603 AC: 91548 AN: 151764 Hom.: 28339 Cov.: 30 AF XY: 0.605 AC XY: 44866 AN XY: 74152

African (AFR) AF: 0.447 AC: 18500 AN: 41344

American (AMR) AF: 0.588 AC: 8955 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.610 AC: 2117 AN: 3470

East Asian (EAS) AF: 0.776 AC: 4005 AN: 5162

South Asian (SAS) AF: 0.622 AC: 2981 AN: 4796

European-Finnish (FIN) AF: 0.628 AC: 6594 AN: 10506

Middle Eastern (MID) AF: 0.711 AC: 209 AN: 294

European-Non Finnish (NFE) AF: 0.680 AC: 46184 AN: 67944

Other (OTH) AF: 0.632 AC: 1331 AN: 2106

Alfa AF: 0.631 Hom.: 3808

Bravo AF: 0.595

Asia WGS AF: 0.647 AC: 2247 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.29
DANN	Benign	0.48
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs9353527; hg19: chr6-88880039;