rs9268530

Variant names:

• chr6-32415446-T-C
• rs9268530
• ENST00000766247.1:n.282+1076T>C

Variant summary

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

The ENST00000766247.1(ENSG00000299769):​n.282+1076T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.127 in 152,200 control chromosomes in the GnomAD database, including 1,510 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 0.13 (1510 hom., cov: 32)
• Consequence: ENSG00000299769 ENST00000766247.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0740
• Publications: 32 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=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.168 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000766247.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000299769	ENST00000766247.1		n.282+1076T>C		intron	N/A
	ENSG00000299769	ENST00000766248.1		n.286+1076T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.127 AC: 19362 AN: 152082 Hom.: 1510 Cov.: 32

Gnomad AFR AF: 0.0665

Gnomad AMI AF: 0.104

Gnomad AMR AF: 0.112

Gnomad ASJ AF: 0.0894

Gnomad EAS AF: 0.0393

Gnomad SAS AF: 0.0459

Gnomad FIN AF: 0.205

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.171

Gnomad OTH AF: 0.120

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

GnomAD4 genome AF: 0.127 AC: 19368 AN: 152200 Hom.: 1510 Cov.: 32 AF XY: 0.124 AC XY: 9260 AN XY: 74408

African (AFR) AF: 0.0667 AC: 2771 AN: 41524

American (AMR) AF: 0.112 AC: 1708 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0894 AC: 310 AN: 3466

East Asian (EAS) AF: 0.0392 AC: 203 AN: 5180

South Asian (SAS) AF: 0.0453 AC: 218 AN: 4814

European-Finnish (FIN) AF: 0.205 AC: 2173 AN: 10590

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.171 AC: 11625 AN: 68012

Other (OTH) AF: 0.119 AC: 250 AN: 2104

Alfa AF: 0.161 Hom.: 5443

Bravo AF: 0.119

Asia WGS AF: 0.0570 AC: 197 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	6.9
DANN	Benign	0.63
PhyloP100		-0.074

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs9268530;

hg19: chr6-32383223;