ENST00000405282.1:n.502T>G

Variant names:

• chr6-150033472-T-G
• rs9479478
• ENST00000405282.1:n.502T>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000405282.1(RAET1M):​n.502T>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 0.443 in 158,960 control chromosomes in the GnomAD database, including 15,884 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 0.44 (15040 hom., cov: 32)
  • Exomes 𝑓: 0.49 (844 hom.)
• Consequence: RAET1M ENST00000405282.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.715
• Publications: 6 publications found

Genes affected

RAET1M (HGNC:16799): (retinoic acid early transcript 1M (pseudogene))

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.467 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RAET1M		n.150033472T>G		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RAET1M	ENST00000405282.1	n.502T>G		non_coding_transcript_exon_variant	Exon 2 of 2	6

Frequencies

GnomAD3 genomes AF: 0.441 AC: 66997 AN: 151768 Hom.: 15030 Cov.: 32

Gnomad AFR AF: 0.473

Gnomad AMI AF: 0.419

Gnomad AMR AF: 0.407

Gnomad ASJ AF: 0.410

Gnomad EAS AF: 0.230

Gnomad SAS AF: 0.417

Gnomad FIN AF: 0.429

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.452

Gnomad OTH AF: 0.432

GnomAD4 exome AF: 0.486 AC: 3440 AN: 7074 Hom.: 844 Cov.: 0 AF XY: 0.487 AC XY: 2052 AN XY: 4214

African (AFR) AF: 0.657 AC: 184 AN: 280

American (AMR) AF: 0.538 AC: 380 AN: 706

Ashkenazi Jewish (ASJ) AF: 0.383 AC: 36 AN: 94

East Asian (EAS) AF: 0.302 AC: 90 AN: 298

South Asian (SAS) AF: 0.503 AC: 335 AN: 666

European-Finnish (FIN) AF: 0.450 AC: 394 AN: 876

Middle Eastern (MID) AF: 0.833 AC: 35 AN: 42

European-Non Finnish (NFE) AF: 0.486 AC: 1805 AN: 3712

Other (OTH) AF: 0.453 AC: 181 AN: 400

GnomAD4 genome AF: 0.441 AC: 67046 AN: 151886 Hom.: 15040 Cov.: 32 AF XY: 0.438 AC XY: 32490 AN XY: 74196

African (AFR) AF: 0.473 AC: 19564 AN: 41368

American (AMR) AF: 0.407 AC: 6223 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.410 AC: 1420 AN: 3466

East Asian (EAS) AF: 0.231 AC: 1190 AN: 5162

South Asian (SAS) AF: 0.417 AC: 2003 AN: 4808

European-Finnish (FIN) AF: 0.429 AC: 4520 AN: 10542

Middle Eastern (MID) AF: 0.418 AC: 123 AN: 294

European-Non Finnish (NFE) AF: 0.452 AC: 30706 AN: 67944

Other (OTH) AF: 0.434 AC: 915 AN: 2106

Alfa AF: 0.440 Hom.: 3324

Bravo AF: 0.441

Asia WGS AF: 0.363 AC: 1262 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.18
DANN	Benign	0.50
PhyloP100		-0.71

Splicing

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

Other links and lift over

dbSNP: rs9479478; hg19: chr6-150354608;