rs4953388

Variant names:

• chr2-46486062-G-A
• rs4953388
• ENST00000517716.2:n.80-13669G>A

Variant summary

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

The ENST00000517716.2(ENSG00000253515):​n.80-13669G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.277 in 152,038 control chromosomes in the GnomAD database, including 7,116 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 0.28 (7116 hom., cov: 32)
• Consequence: ENSG00000253515 ENST00000517716.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.10

Genes affected

ENSG00000253515 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.376 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
ENSG00000253515	ENST00000517716.2	n.80-13669G>A		intron_variant	Intron 2 of 3	5

Frequencies

GnomAD3 genomes AF: 0.278 AC: 42187 AN: 151920 Hom.: 7115 Cov.: 32

Gnomad AFR AF: 0.0973

Gnomad AMI AF: 0.266

Gnomad AMR AF: 0.343

Gnomad ASJ AF: 0.361

Gnomad EAS AF: 0.0777

Gnomad SAS AF: 0.210

Gnomad FIN AF: 0.329

Gnomad MID AF: 0.363

Gnomad NFE AF: 0.380

Gnomad OTH AF: 0.297

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

GnomAD4 genome AF: 0.277 AC: 42184 AN: 152038 Hom.: 7116 Cov.: 32 AF XY: 0.275 AC XY: 20445 AN XY: 74298

Gnomad4 AFR AF: 0.0970

Gnomad4 AMR AF: 0.343

Gnomad4 ASJ AF: 0.361

Gnomad4 EAS AF: 0.0777

Gnomad4 SAS AF: 0.210

Gnomad4 FIN AF: 0.329

Gnomad4 NFE AF: 0.380

Gnomad4 OTH AF: 0.293

Alfa AF: 0.350 Hom.: 5957

Bravo AF: 0.269

Asia WGS AF: 0.159 AC: 554 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.6
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4953388; hg19: chr2-46713201;