rs17374222

Positions:

• chr15-69703005-C-A
• chr15-69703005-C-T

Variant summary

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

The ENST00000558941.6(DRAIC):​n.7802C>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 0.55 in 151,928 control chromosomes in the GnomAD database, including 23,372 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 0.55 (23368 hom., cov: 31)
  • Exomes 𝑓: 0.33 (4 hom.)
• Consequence: DRAIC ENST00000558941.6 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.605

Genes affected

DRAIC (HGNC:27082): (downregulated RNA in cancer, inhibitor of cell invasion and migration)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.75 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
DRAIC	ENST00000558941.6	n.7802C>A		non_coding_transcript_exon_variant	5/5	4
DRAIC	ENST00000647319.1	n.721+3120C>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.550 AC: 83442 AN: 151770 Hom.: 23321 Cov.: 31

Gnomad AFR AF: 0.613

Gnomad AMI AF: 0.776

Gnomad AMR AF: 0.610

Gnomad ASJ AF: 0.499

Gnomad EAS AF: 0.770

Gnomad SAS AF: 0.450

Gnomad FIN AF: 0.532

Gnomad MID AF: 0.636

Gnomad NFE AF: 0.490

Gnomad OTH AF: 0.576

GnomAD4 exome AF: 0.325 AC: 13 AN: 40 Hom.: 4 Cov.: 0 AF XY: 0.342 AC XY: 13 AN XY: 38

Gnomad4 AFR exome AF: 0.00

Gnomad4 NFE exome AF: 0.281

Gnomad4 OTH exome AF: 1.00

GnomAD4 genome AF: 0.550 AC: 83531 AN: 151888 Hom.: 23368 Cov.: 31 AF XY: 0.553 AC XY: 41036 AN XY: 74238

Gnomad4 AFR AF: 0.613

Gnomad4 AMR AF: 0.610

Gnomad4 ASJ AF: 0.499

Gnomad4 EAS AF: 0.771

Gnomad4 SAS AF: 0.450

Gnomad4 FIN AF: 0.532

Gnomad4 NFE AF: 0.490

Gnomad4 OTH AF: 0.576

Alfa AF: 0.505 Hom.: 23095

Bravo AF: 0.567

Asia WGS AF: 0.580 AC: 2018 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.44
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17374222; hg19: chr15-69995344;