rs12657273

Variant names:

• chr5-107710997-T-C
• rs12657273
• ENST00000502287.1:n.210-489A>G

Your query was ambiguous. Multiple possible variants found:

• chr5-107710997-T-C
• chr5-107710997-T-G

Variant summary

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

The ENST00000509458.5(ENSG00000249959):​n.75-489A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.393 in 151,972 control chromosomes in the GnomAD database, including 11,872 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 0.39 (11872 hom., cov: 32)
• Consequence: ENSG00000249959 ENST00000509458.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.21

Genes affected

ENSG00000249959 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.525 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
ENSG00000249959	ENST00000502287.1	n.210-489A>G		intron_variant	Intron 1 of 4	5
ENSG00000249959	ENST00000509458.5	n.75-489A>G		intron_variant	Intron 1 of 4	3

Frequencies

GnomAD3 genomes AF: 0.393 AC: 59675 AN: 151854 Hom.: 11867 Cov.: 32

Gnomad AFR AF: 0.336

Gnomad AMI AF: 0.424

Gnomad AMR AF: 0.421

Gnomad ASJ AF: 0.408

Gnomad EAS AF: 0.374

Gnomad SAS AF: 0.542

Gnomad FIN AF: 0.373

Gnomad MID AF: 0.440

Gnomad NFE AF: 0.414

Gnomad OTH AF: 0.384

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

GnomAD4 genome AF: 0.393 AC: 59706 AN: 151972 Hom.: 11872 Cov.: 32 AF XY: 0.394 AC XY: 29281 AN XY: 74296

Gnomad4 AFR AF: 0.335

Gnomad4 AMR AF: 0.421

Gnomad4 ASJ AF: 0.408

Gnomad4 EAS AF: 0.374

Gnomad4 SAS AF: 0.543

Gnomad4 FIN AF: 0.373

Gnomad4 NFE AF: 0.414

Gnomad4 OTH AF: 0.380

Alfa AF: 0.411 Hom.: 6917

Bravo AF: 0.390

Asia WGS AF: 0.396 AC: 1375 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	6.8
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12657273; hg19: chr5-107046698;