rs1427828

chr12-89368722-C-G

Variant summary

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

The ENST00000605595.1(ENSG00000271327):n.916C>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.469 in 152,048 control chromosomes in the GnomAD database, including 17,902 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 0.47 (17890 hom., cov: 32)
  • Exomes 𝑓: 0.71 (12 hom.)
• Consequence: ENST00000605595.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.300

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.588 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
	ENST00000605595.1	n.916C>G		non_coding_transcript_exon_variant	1/1
	ENST00000657284.1	n.123+14802C>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.469 AC: 71230 AN: 151894 Hom.: 17891 Cov.: 32

Gnomad AFR AF: 0.278

Gnomad AMI AF: 0.557

Gnomad AMR AF: 0.491

Gnomad ASJ AF: 0.515

Gnomad EAS AF: 0.606

Gnomad SAS AF: 0.506

Gnomad FIN AF: 0.630

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.538

Gnomad OTH AF: 0.478

GnomAD4 exome AF: 0.711 AC: 27 AN: 38 Hom.: 12 Cov.: 0 AF XY: 0.731 AC XY: 19 AN XY: 26

Gnomad4 AFR exome AF: 0.00

Gnomad4 ASJ exome AF: 1.00

Gnomad4 SAS exome AF: 0.500

Gnomad4 FIN exome AF: 1.00

Gnomad4 NFE exome AF: 0.750

Gnomad4 OTH exome AF: 0.750

GnomAD4 genome AF: 0.469 AC: 71248 AN: 152010 Hom.: 17890 Cov.: 32 AF XY: 0.475 AC XY: 35307 AN XY: 74294

Gnomad4 AFR AF: 0.278

Gnomad4 AMR AF: 0.490

Gnomad4 ASJ AF: 0.515

Gnomad4 EAS AF: 0.606

Gnomad4 SAS AF: 0.507

Gnomad4 FIN AF: 0.630

Gnomad4 NFE AF: 0.538

Gnomad4 OTH AF: 0.483

Alfa AF: 0.487 Hom.: 2341

Bravo AF: 0.453

Asia WGS AF: 0.570 AC: 1980 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	1.7
Dann	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1427828; hg19: chr12-89762499;