rs12657273

Positions:

• 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 ENST00000502287.1(ENSG00000249959):​n.210-489A>G 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 0.393 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: ENST00000502287.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.21

Genes affected

(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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000502287.1	n.210-489A>G		intron_variant, non_coding_transcript_variant		5
	ENST00000509458.5	n.75-489A>G		intron_variant, non_coding_transcript_variant		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;