rs13410351

Positions:

• chr2-103141683-G-T

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, non coding transcript 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: ENST00000422683.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.86

Genes affected

(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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000422683.1	n.214-24778C>A		intron_variant, non_coding_transcript_variant		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;