6-150033472-T-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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000405282.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RAET1M	ENST00000405282.1	TSL:6	n.502T>G		non_coding_transcript_exon	Exon 2 of 2

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs9479478;

hg19: chr6-150354608;