rs9268528

Variant names:

• chr6-32415331-A-G
• rs9268528
• ENST00000766247.1:n.282+961A>G

Your query was ambiguous. Multiple possible variants found:

• chr6-32415331-A-G
• chr6-32415331-A-T

Variant summary

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

The ENST00000766247.1(ENSG00000299769):​n.282+961A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.35 in 151,918 control chromosomes in the GnomAD database, including 9,921 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 (9921 hom., cov: 31)
• Consequence: ENSG00000299769 ENST00000766247.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.782
• Publications: 51 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=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.484 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+961A>G		intron_variant	Intron 2 of 2
ENSG00000299769	ENST00000766248.1	n.286+961A>G		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.350 AC: 53167 AN: 151800 Hom.: 9915 Cov.: 31

Gnomad AFR AF: 0.237

Gnomad AMI AF: 0.334

Gnomad AMR AF: 0.426

Gnomad ASJ AF: 0.525

Gnomad EAS AF: 0.476

Gnomad SAS AF: 0.500

Gnomad FIN AF: 0.306

Gnomad MID AF: 0.592

Gnomad NFE AF: 0.379

Gnomad OTH AF: 0.365

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

GnomAD4 genome AF: 0.350 AC: 53192 AN: 151918 Hom.: 9921 Cov.: 31 AF XY: 0.354 AC XY: 26254 AN XY: 74218

African (AFR) AF: 0.237 AC: 9839 AN: 41458

American (AMR) AF: 0.426 AC: 6497 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.525 AC: 1820 AN: 3468

East Asian (EAS) AF: 0.477 AC: 2442 AN: 5122

South Asian (SAS) AF: 0.500 AC: 2401 AN: 4798

European-Finnish (FIN) AF: 0.306 AC: 3224 AN: 10540

Middle Eastern (MID) AF: 0.582 AC: 171 AN: 294

European-Non Finnish (NFE) AF: 0.379 AC: 25723 AN: 67952

Other (OTH) AF: 0.365 AC: 772 AN: 2114

Alfa AF: 0.377 Hom.: 42575

Bravo AF: 0.354

Asia WGS AF: 0.436 AC: 1518 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.4
DANN	Benign	0.35
PhyloP100		-0.78

Splicing

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

Other links and lift over

dbSNP: rs9268528; hg19: chr6-32383108;