ENST00000558941.6:n.7802C>A

Variant names:

• chr15-69703005-C-A
• rs17374222
• ENST00000558941.6:n.7802C>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 17 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000558941.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DRAIC	ENST00000558941.6	TSL:4	n.7802C>A		non_coding_transcript_exon	Exon 5 of 5
	DRAIC	ENST00000647319.1		n.721+3120C>A		intron	N/A

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

African (AFR) AF: 0.00 AC: 0 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2

European-Non Finnish (NFE) AF: 0.281 AC: 9 AN: 32

Other (OTH) AF: 1.00 AC: 4 AN: 4

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

African (AFR) AF: 0.613 AC: 25381 AN: 41404

American (AMR) AF: 0.610 AC: 9320 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.499 AC: 1731 AN: 3470

East Asian (EAS) AF: 0.771 AC: 3965 AN: 5146

South Asian (SAS) AF: 0.450 AC: 2168 AN: 4816

European-Finnish (FIN) AF: 0.532 AC: 5603 AN: 10536

Middle Eastern (MID) AF: 0.619 AC: 182 AN: 294

European-Non Finnish (NFE) AF: 0.490 AC: 33258 AN: 67932

Other (OTH) AF: 0.576 AC: 1215 AN: 2110

Alfa AF: 0.519 Hom.: 42423

Bravo AF: 0.567

Asia WGS AF: 0.580 AC: 2018 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.44
DANN	Benign	0.51
PhyloP100		-0.60

Splicing

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

Other links and lift over

dbSNP: rs17374222; hg19: chr15-69995344;