rs13410282

Variant names:

• chr2-201106301-G-A
• rs13410282
• ENST00000832402.1:n.188-498C>T

Variant summary

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

The ENST00000832402.1(ENSG00000308192):​n.188-498C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.307 in 151,958 control chromosomes in the GnomAD database, including 9,285 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 0.31 (9285 hom., cov: 32)
• Consequence: ENSG00000308192 ENST00000832402.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.136
• Publications: 16 publications found

Genes affected

ENSG00000308192 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.556 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105373836	XR_923785.3	n.1838-498C>T		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000308192	ENST00000832402.1	n.188-498C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.306 AC: 46525 AN: 151842 Hom.: 9261 Cov.: 32

Gnomad AFR AF: 0.562

Gnomad AMI AF: 0.178

Gnomad AMR AF: 0.205

Gnomad ASJ AF: 0.335

Gnomad EAS AF: 0.0135

Gnomad SAS AF: 0.144

Gnomad FIN AF: 0.205

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.225

Gnomad OTH AF: 0.280

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

GnomAD4 genome AF: 0.307 AC: 46608 AN: 151958 Hom.: 9285 Cov.: 32 AF XY: 0.302 AC XY: 22402 AN XY: 74274

African (AFR) AF: 0.562 AC: 23258 AN: 41398

American (AMR) AF: 0.205 AC: 3127 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.335 AC: 1164 AN: 3470

East Asian (EAS) AF: 0.0135 AC: 70 AN: 5182

South Asian (SAS) AF: 0.143 AC: 690 AN: 4820

European-Finnish (FIN) AF: 0.205 AC: 2167 AN: 10562

Middle Eastern (MID) AF: 0.221 AC: 65 AN: 294

European-Non Finnish (NFE) AF: 0.225 AC: 15302 AN: 67960

Other (OTH) AF: 0.286 AC: 603 AN: 2110

Alfa AF: 0.278 Hom.: 10997

Bravo AF: 0.317

Asia WGS AF: 0.129 AC: 452 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.45
DANN	Benign	0.23
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs13410282; hg19: chr2-201971024;