rs9268542

Variant names:

• chr6-32416944-A-G
• rs9268542
• ENST00000766247.1:n.282+2574A>G

Variant summary

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

The ENST00000766247.1(ENSG00000299769):​n.282+2574A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.353 in 152,062 control chromosomes in the GnomAD database, including 10,105 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 0.35 (10105 hom., cov: 32)
• Consequence: ENSG00000299769 ENST00000766247.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0970
• Publications: 62 publications found

Genes affected

ENSG00000299769 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.485 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
ENSG00000299769	ENST00000766247.1	n.282+2574A>G		intron_variant	Intron 2 of 2
ENSG00000299769	ENST00000766248.1	n.286+2574A>G		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.353 AC: 53643 AN: 151942 Hom.: 10098 Cov.: 32

Gnomad AFR AF: 0.236

Gnomad AMI AF: 0.348

Gnomad AMR AF: 0.430

Gnomad ASJ AF: 0.537

Gnomad EAS AF: 0.473

Gnomad SAS AF: 0.501

Gnomad FIN AF: 0.307

Gnomad MID AF: 0.596

Gnomad NFE AF: 0.383

Gnomad OTH AF: 0.367

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

GnomAD4 genome AF: 0.353 AC: 53664 AN: 152062 Hom.: 10105 Cov.: 32 AF XY: 0.356 AC XY: 26479 AN XY: 74320

African (AFR) AF: 0.236 AC: 9805 AN: 41486

American (AMR) AF: 0.430 AC: 6571 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.537 AC: 1864 AN: 3470

East Asian (EAS) AF: 0.474 AC: 2453 AN: 5176

South Asian (SAS) AF: 0.501 AC: 2416 AN: 4818

European-Finnish (FIN) AF: 0.307 AC: 3239 AN: 10536

Middle Eastern (MID) AF: 0.586 AC: 171 AN: 292

European-Non Finnish (NFE) AF: 0.383 AC: 26051 AN: 67990

Other (OTH) AF: 0.368 AC: 777 AN: 2114

Alfa AF: 0.384 Hom.: 33671

Bravo AF: 0.357

Asia WGS AF: 0.436 AC: 1511 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	5.5
DANN	Benign	0.71
PhyloP100		0.097

Splicing

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

Other links and lift over

dbSNP: rs9268542; hg19: chr6-32384721;