rs13410351

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 0 publications found

Genes affected

ENSG00000229209 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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
ENSG00000300106	ENST00000768846.1	n.65+8878G>T		intron_variant	Intron 1 of 1
ENSG00000300106	ENST00000768847.1	n.51+8878G>T		intron_variant	Intron 1 of 1

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

African (AFR) AF: 0.472 AC: 19567 AN: 41434

American (AMR) AF: 0.144 AC: 2199 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0959 AC: 333 AN: 3472

East Asian (EAS) AF: 0.397 AC: 2051 AN: 5164

South Asian (SAS) AF: 0.125 AC: 604 AN: 4820

European-Finnish (FIN) AF: 0.141 AC: 1500 AN: 10612

Middle Eastern (MID) AF: 0.0856 AC: 25 AN: 292

European-Non Finnish (NFE) AF: 0.0467 AC: 3177 AN: 68010

Other (OTH) AF: 0.165 AC: 348 AN: 2110

Alfa AF: 0.0846 Hom.: 1019

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
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs13410351; hg19: chr2-103758141;