rs12431307

Positions:

• 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 ENST00000648514.1(ENSG00000284196):​n.298-669C>T 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 0.416 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: ENST00000648514.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.68

Genes affected

(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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000648514.1	n.298-669C>T		intron_variant, non_coding_transcript_variant

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;