rs1427828

Variant names:

• chr12-89368722-C-G
• rs1427828
• ENST00000605595.1:n.916C>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: ENSG00000271327 ENST00000605595.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.300

Genes affected

ENSG00000271327 (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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000271327	ENST00000605595.1	n.916C>G		non_coding_transcript_exon_variant	Exon 1 of 1	6
ENSG00000286608	ENST00000657284.1	n.123+14802C>G		intron_variant	Intron 1 of 2

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;