rs1336333

Variant names:

• chr9-26783850-G-C
• rs1336333
• ENST00000523363.2:n.355-2936G>C

Variant summary

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

The ENST00000523363.2(ENSG00000254261):​n.355-2936G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.242 in 152,052 control chromosomes in the GnomAD database, including 4,878 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 0.24 (4878 hom., cov: 32)
• Consequence: ENSG00000254261 ENST00000523363.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.233
• Publications: 1 publications found

Genes affected

ENSG00000254261 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.275 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
ENSG00000254261	ENST00000523363.2	n.355-2936G>C		intron_variant	Intron 3 of 5	3

Frequencies

GnomAD3 genomes AF: 0.242 AC: 36793 AN: 151934 Hom.: 4867 Cov.: 32

Gnomad AFR AF: 0.221

Gnomad AMI AF: 0.211

Gnomad AMR AF: 0.282

Gnomad ASJ AF: 0.329

Gnomad EAS AF: 0.00386

Gnomad SAS AF: 0.0721

Gnomad FIN AF: 0.249

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.272

Gnomad OTH AF: 0.215

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

GnomAD4 genome AF: 0.242 AC: 36830 AN: 152052 Hom.: 4878 Cov.: 32 AF XY: 0.235 AC XY: 17498 AN XY: 74320

African (AFR) AF: 0.222 AC: 9195 AN: 41462

American (AMR) AF: 0.282 AC: 4308 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.329 AC: 1141 AN: 3470

East Asian (EAS) AF: 0.00386 AC: 20 AN: 5176

South Asian (SAS) AF: 0.0718 AC: 346 AN: 4822

European-Finnish (FIN) AF: 0.249 AC: 2628 AN: 10556

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.272 AC: 18521 AN: 67970

Other (OTH) AF: 0.213 AC: 448 AN: 2108

Alfa AF: 0.271 Hom.: 698

Bravo AF: 0.246

Asia WGS AF: 0.0620 AC: 216 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.6
DANN	Benign	0.35
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs1336333; hg19: chr9-26783848;