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. The variant received -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
• Publications: 6 publications found

Genes affected

ENSG00000249959 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000509458.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000249959	ENST00000502287.1	TSL:5	n.210-489A>G		intron	N/A
	ENSG00000249959	ENST00000509458.5	TSL:3	n.75-489A>G		intron	N/A

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

African (AFR) AF: 0.335 AC: 13893 AN: 41430

American (AMR) AF: 0.421 AC: 6429 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.408 AC: 1416 AN: 3468

East Asian (EAS) AF: 0.374 AC: 1936 AN: 5172

South Asian (SAS) AF: 0.543 AC: 2614 AN: 4816

European-Finnish (FIN) AF: 0.373 AC: 3940 AN: 10562

Middle Eastern (MID) AF: 0.442 AC: 130 AN: 294

European-Non Finnish (NFE) AF: 0.414 AC: 28157 AN: 67938

Other (OTH) AF: 0.380 AC: 804 AN: 2114

Alfa AF: 0.410 Hom.: 7585

Bravo AF: 0.390

Asia WGS AF: 0.396 AC: 1375 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	6.8
DANN	Benign	0.73
PhyloP100		1.2

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs12657273;

hg19: chr5-107046698;