rs13410351

Variant names:

• chr2-103141683-G-T
• rs13410351
• ENST00000422683.1:n.214-24778C>A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000422683.1(ENSG00000229209):​n.214-24778C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.196 in 152,124 control chromosomes in the GnomAD database, including 5,595 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 0.20 (5595 hom., cov: 32)
• Consequence: ENSG00000229209 ENST00000422683.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.86

Genes affected

ENSG00000229209 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.467 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
ENSG00000229209	ENST00000422683.1	n.214-24778C>A		intron_variant	Intron 2 of 3	3

Frequencies

GnomAD3 genomes AF: 0.196 AC: 29749 AN: 152006 Hom.: 5576 Cov.: 32

Gnomad AFR AF: 0.472

Gnomad AMI AF: 0.0275

Gnomad AMR AF: 0.143

Gnomad ASJ AF: 0.0959

Gnomad EAS AF: 0.397

Gnomad SAS AF: 0.126

Gnomad FIN AF: 0.141

Gnomad MID AF: 0.0796

Gnomad NFE AF: 0.0467

Gnomad OTH AF: 0.159

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

GnomAD4 genome AF: 0.196 AC: 29829 AN: 152124 Hom.: 5595 Cov.: 32 AF XY: 0.199 AC XY: 14792 AN XY: 74366

Gnomad4 AFR AF: 0.472

Gnomad4 AMR AF: 0.144

Gnomad4 ASJ AF: 0.0959

Gnomad4 EAS AF: 0.397

Gnomad4 SAS AF: 0.125

Gnomad4 FIN AF: 0.141

Gnomad4 NFE AF: 0.0467

Gnomad4 OTH AF: 0.165

Alfa AF: 0.0814 Hom.: 689

Bravo AF: 0.213

Asia WGS AF: 0.301 AC: 1043 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	0.021
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13410351; hg19: chr2-103758141;