rs312732

Positions:

• chr17-70313179-G-T

Variant summary

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

The ENST00000592809.1(ENSG00000267109):​n.386C>A 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 0.248 in 152,010 control chromosomes in the GnomAD database, including 4,929 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 0.25 (4929 hom., cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: ENST00000592809.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.16

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.462 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
	ENST00000592809.1	n.386C>A		non_coding_transcript_exon_variant	3/3	3

Frequencies

GnomAD3 genomes AF: 0.248 AC: 37732 AN: 151894 Hom.: 4917 Cov.: 32

Gnomad AFR AF: 0.242

Gnomad AMI AF: 0.268

Gnomad AMR AF: 0.295

Gnomad ASJ AF: 0.289

Gnomad EAS AF: 0.477

Gnomad SAS AF: 0.172

Gnomad FIN AF: 0.172

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.239

Gnomad OTH AF: 0.245

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 4 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 4

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.248 AC: 37762 AN: 152010 Hom.: 4929 Cov.: 32 AF XY: 0.247 AC XY: 18359 AN XY: 74296

Gnomad4 AFR AF: 0.242

Gnomad4 AMR AF: 0.296

Gnomad4 ASJ AF: 0.289

Gnomad4 EAS AF: 0.478

Gnomad4 SAS AF: 0.172

Gnomad4 FIN AF: 0.172

Gnomad4 NFE AF: 0.239

Gnomad4 OTH AF: 0.245

Alfa AF: 0.238 Hom.: 556

Bravo AF: 0.264

Asia WGS AF: 0.310 AC: 1077 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.20
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs312732; hg19: chr17-68309320;