rs12431307

Variant names:

• chr13-80070483-G-A
• rs12431307
• ENST00000639897.1:n.189-669C>T

Your query was ambiguous. Multiple possible variants found:

• chr13-80070483-G-A
• chr13-80070483-G-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000639964.1(ENSG00000284196):​n.186-46C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.416 in 151,948 control chromosomes in the GnomAD database, including 13,762 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 0.42 (13761 hom., cov: 32)
  • Exomes 𝑓: 0.36 (1 hom.)
• Consequence: ENSG00000284196 ENST00000639964.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.68

Genes affected

ENSG00000284196 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.34).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.703 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
ENSG00000284196	ENST00000639897.1	n.189-669C>T		intron_variant	Intron 2 of 8	5
ENSG00000284196	ENST00000639964.1	n.186-46C>T		intron_variant	Intron 2 of 5	4
ENSG00000284196	ENST00000639965.1	n.214+2906C>T		intron_variant	Intron 2 of 5	5

Frequencies

GnomAD3 genomes AF: 0.416 AC: 63146 AN: 151802 Hom.: 13757 Cov.: 32

Gnomad AFR AF: 0.304

Gnomad AMI AF: 0.384

Gnomad AMR AF: 0.529

Gnomad ASJ AF: 0.447

Gnomad EAS AF: 0.722

Gnomad SAS AF: 0.402

Gnomad FIN AF: 0.391

Gnomad MID AF: 0.378

Gnomad NFE AF: 0.439

Gnomad OTH AF: 0.431

GnomAD4 exome AF: 0.357 AC: 10 AN: 28 Hom.: 1 Cov.: 0 AF XY: 0.313 AC XY: 5 AN XY: 16

Gnomad4 AFR exome AF: 0.00

Gnomad4 FIN exome AF: 0.500

Gnomad4 NFE exome AF: 0.389

Gnomad4 OTH exome AF: 0.250

GnomAD4 genome AF: 0.416 AC: 63170 AN: 151920 Hom.: 13761 Cov.: 32 AF XY: 0.420 AC XY: 31159 AN XY: 74224

Gnomad4 AFR AF: 0.303

Gnomad4 AMR AF: 0.530

Gnomad4 ASJ AF: 0.447

Gnomad4 EAS AF: 0.722

Gnomad4 SAS AF: 0.402

Gnomad4 FIN AF: 0.391

Gnomad4 NFE AF: 0.439

Gnomad4 OTH AF: 0.427

Alfa AF: 0.441 Hom.: 30813

Bravo AF: 0.425

Asia WGS AF: 0.489 AC: 1697 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.34
CADD	Benign	11
DANN	Benign	0.87

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12431307; hg19: chr13-80644618;