rs9268560

Variant names:

• chr6-32421735-C-G
• rs9268560
• ENST00000766247.1:n.282+7365C>G

Your query was ambiguous. Multiple possible variants found:

• chr6-32421735-C-G
• chr6-32421735-C-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+7365C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.555 in 151,972 control chromosomes in the GnomAD database, including 23,599 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 0.55 (23599 hom., cov: 31)
• Consequence: ENSG00000299769 ENST00000766247.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.710
• Publications: 21 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=-0.86).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.603 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+7365C>G		intron_variant	Intron 2 of 2
ENSG00000299769	ENST00000766248.1	n.287-3633C>G		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.555 AC: 84238 AN: 151854 Hom.: 23577 Cov.: 31

Gnomad AFR AF: 0.546

Gnomad AMI AF: 0.575

Gnomad AMR AF: 0.613

Gnomad ASJ AF: 0.719

Gnomad EAS AF: 0.532

Gnomad SAS AF: 0.602

Gnomad FIN AF: 0.536

Gnomad MID AF: 0.782

Gnomad NFE AF: 0.537

Gnomad OTH AF: 0.590

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

GnomAD4 genome AF: 0.555 AC: 84298 AN: 151972 Hom.: 23599 Cov.: 31 AF XY: 0.558 AC XY: 41458 AN XY: 74274

African (AFR) AF: 0.546 AC: 22616 AN: 41440

American (AMR) AF: 0.613 AC: 9369 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.719 AC: 2495 AN: 3472

East Asian (EAS) AF: 0.533 AC: 2755 AN: 5172

South Asian (SAS) AF: 0.604 AC: 2897 AN: 4798

European-Finnish (FIN) AF: 0.536 AC: 5647 AN: 10530

Middle Eastern (MID) AF: 0.772 AC: 227 AN: 294

European-Non Finnish (NFE) AF: 0.537 AC: 36518 AN: 67962

Other (OTH) AF: 0.592 AC: 1251 AN: 2112

Alfa AF: 0.425 Hom.: 1206

Bravo AF: 0.561

Asia WGS AF: 0.559 AC: 1948 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	4.6
DANN	Benign	0.71
PhyloP100		0.71

Splicing

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

Other links and lift over

dbSNP: rs9268560; hg19: chr6-32389512;