rs2310333

Variant names:

• chr9-73092464-A-G
• rs2310333
• ENST00000715863.1:n.376-467T>C

Variant summary

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

The ENST00000715863.1(ENSG00000293607):​n.376-467T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.606 in 151,866 control chromosomes in the GnomAD database, including 28,994 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 0.61 (28994 hom., cov: 31)
• Consequence: ENSG00000293607 ENST00000715863.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.323
• Publications: 4 publications found

Genes affected

ENSG00000293607 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.679 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105376081	XR_929926.2	n.407-467T>C		intron_variant	Intron 3 of 3
LOC105376081	XR_929927.2	n.344-467T>C		intron_variant	Intron 3 of 3
LOC105376081	XR_929928.2	n.216-467T>C		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000293607	ENST00000715863.1	n.376-467T>C		intron_variant	Intron 3 of 3
ENSG00000293607	ENST00000719114.1	n.320-467T>C		intron_variant	Intron 2 of 2
ENSG00000293607	ENST00000719115.1	n.247-467T>C		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.606 AC: 91922 AN: 151746 Hom.: 28972 Cov.: 31

Gnomad AFR AF: 0.427

Gnomad AMI AF: 0.732

Gnomad AMR AF: 0.655

Gnomad ASJ AF: 0.617

Gnomad EAS AF: 0.458

Gnomad SAS AF: 0.673

Gnomad FIN AF: 0.747

Gnomad MID AF: 0.627

Gnomad NFE AF: 0.685

Gnomad OTH AF: 0.642

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

GnomAD4 genome AF: 0.606 AC: 91994 AN: 151866 Hom.: 28994 Cov.: 31 AF XY: 0.610 AC XY: 45294 AN XY: 74216

African (AFR) AF: 0.427 AC: 17691 AN: 41426

American (AMR) AF: 0.655 AC: 9991 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.617 AC: 2140 AN: 3466

East Asian (EAS) AF: 0.458 AC: 2361 AN: 5156

South Asian (SAS) AF: 0.674 AC: 3251 AN: 4820

European-Finnish (FIN) AF: 0.747 AC: 7878 AN: 10546

Middle Eastern (MID) AF: 0.626 AC: 184 AN: 294

European-Non Finnish (NFE) AF: 0.685 AC: 46482 AN: 67888

Other (OTH) AF: 0.639 AC: 1348 AN: 2110

Alfa AF: 0.662 Hom.: 16986

Bravo AF: 0.588

Asia WGS AF: 0.565 AC: 1969 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.80
DANN	Benign	0.51
PhyloP100		-0.32

Splicing

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

Other links and lift over

dbSNP: rs2310333; hg19: chr9-75707380;