rs13285401

Variant names:

• chr9-35152861-T-C
• rs13285401
• ENST00000836210.1:n.423-1258A>G

Variant summary

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

The ENST00000836210.1(ENSG00000308740):​n.423-1258A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.549 in 151,598 control chromosomes in the GnomAD database, including 23,845 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 (23845 hom., cov: 29)
• Consequence: ENSG00000308740 ENST00000836210.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.07
• Publications: 2 publications found

Genes affected

ENSG00000308740 (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 = 0.621 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124902147	XR_007061468.1	n.340-1258A>G		intron_variant	Intron 1 of 1
LOC124902147	XR_007061469.1	n.340-1262A>G		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000308740	ENST00000836210.1	n.423-1258A>G		intron_variant	Intron 2 of 2
ENSG00000308740	ENST00000836211.1	n.723-1258A>G		intron_variant	Intron 2 of 2
ENSG00000308740	ENST00000836212.1	n.963-1258A>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.549 AC: 83224 AN: 151478 Hom.: 23826 Cov.: 29

Gnomad AFR AF: 0.428

Gnomad AMI AF: 0.557

Gnomad AMR AF: 0.618

Gnomad ASJ AF: 0.640

Gnomad EAS AF: 0.225

Gnomad SAS AF: 0.366

Gnomad FIN AF: 0.639

Gnomad MID AF: 0.599

Gnomad NFE AF: 0.626

Gnomad OTH AF: 0.559

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

GnomAD4 genome AF: 0.549 AC: 83281 AN: 151598 Hom.: 23845 Cov.: 29 AF XY: 0.544 AC XY: 40252 AN XY: 74042

African (AFR) AF: 0.428 AC: 17656 AN: 41262

American (AMR) AF: 0.619 AC: 9413 AN: 15218

Ashkenazi Jewish (ASJ) AF: 0.640 AC: 2222 AN: 3472

East Asian (EAS) AF: 0.224 AC: 1153 AN: 5136

South Asian (SAS) AF: 0.366 AC: 1756 AN: 4794

European-Finnish (FIN) AF: 0.639 AC: 6699 AN: 10490

Middle Eastern (MID) AF: 0.599 AC: 175 AN: 292

European-Non Finnish (NFE) AF: 0.626 AC: 42529 AN: 67920

Other (OTH) AF: 0.557 AC: 1171 AN: 2104

Alfa AF: 0.587 Hom.: 3359

Bravo AF: 0.543

Asia WGS AF: 0.310 AC: 1080 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.0
DANN	Benign	0.35
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs13285401; hg19: chr9-35152858;