rs9501626

Variant names:

• chr6-32432567-C-A
• rs9501626
• ENST00000766007.1:n.280-1836G>T

Your query was ambiguous. Multiple possible variants found:

• chr6-32432567-C-A
• chr6-32432567-C-T

Variant summary

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

The ENST00000766007.1(ENSG00000299747):​n.280-1836G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.173 in 152,050 control chromosomes in the GnomAD database, including 2,859 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 0.17 (2859 hom., cov: 32)
• Consequence: ENSG00000299747 ENST00000766007.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.609
• Publications: 37 publications found

Genes affected

ENSG00000299747 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.289 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
ENSG00000299747	ENST00000766007.1	n.280-1836G>T		intron_variant	Intron 2 of 2
ENSG00000299769	ENST00000766247.1	n.283-1525C>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.172 AC: 26199 AN: 151932 Hom.: 2849 Cov.: 32

Gnomad AFR AF: 0.293

Gnomad AMI AF: 0.0526

Gnomad AMR AF: 0.203

Gnomad ASJ AF: 0.188

Gnomad EAS AF: 0.146

Gnomad SAS AF: 0.119

Gnomad FIN AF: 0.117

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.108

Gnomad OTH AF: 0.178

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

GnomAD4 genome AF: 0.173 AC: 26239 AN: 152050 Hom.: 2859 Cov.: 32 AF XY: 0.170 AC XY: 12611 AN XY: 74326

African (AFR) AF: 0.293 AC: 12137 AN: 41430

American (AMR) AF: 0.204 AC: 3116 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.188 AC: 652 AN: 3472

East Asian (EAS) AF: 0.145 AC: 752 AN: 5174

South Asian (SAS) AF: 0.119 AC: 575 AN: 4826

European-Finnish (FIN) AF: 0.117 AC: 1238 AN: 10572

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.108 AC: 7320 AN: 67980

Other (OTH) AF: 0.178 AC: 376 AN: 2112

Alfa AF: 0.130 Hom.: 6243

Bravo AF: 0.188

Asia WGS AF: 0.168 AC: 582 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.47
DANN	Benign	0.17
PhyloP100		-0.61

Splicing

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

Other links and lift over

dbSNP: rs9501626; hg19: chr6-32400344;