rs6712

Variant names:

• chr22-50199493-G-A
• rs6712
• ENST00000463233.1:n.2302G>A

Your query was ambiguous. Multiple possible variants found:

• chr22-50199493-G-A
• chr22-50199493-G-C

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000463233.1(TRABD):​n.2302G>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 0.0000592 in 202,620 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.000066 (0 hom., cov: 34)
  • Exomes 𝑓: 0.000040 (0 hom.)
• Consequence: TRABD ENST00000463233.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.38
• Publications: 15 publications found

Genes affected

TRABD (HGNC:28805): (TraB domain containing)

TRABD-AS1 (HGNC:56049): (TRABD antisense RNA 1)

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TRABD	NM_001320485.2	c.*974G>A		3_prime_UTR_variant	Exon 10 of 10	ENST00000380909.9	NP_001307414.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TRABD	ENST00000380909.9	c.*974G>A		3_prime_UTR_variant	Exon 10 of 10	5	NM_001320485.2	ENSP00000370295.4

Frequencies

GnomAD3 genomes AF: 0.0000657 AC: 10 AN: 152214 Hom.: 0 Cov.: 34

Gnomad AFR AF: 0.0000241

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000131

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.0000942

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000882

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.0000398 AC: 2 AN: 50288 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 25248

African (AFR) AF: 0.00 AC: 0 AN: 1996

American (AMR) AF: 0.00 AC: 0 AN: 1384

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2178

East Asian (EAS) AF: 0.00 AC: 0 AN: 3334

South Asian (SAS) AF: 0.00 AC: 0 AN: 1522

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 2260

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 288

European-Non Finnish (NFE) AF: 0.0000595 AC: 2 AN: 33608

Other (OTH) AF: 0.00 AC: 0 AN: 3718

GnomAD4 genome AF: 0.0000656 AC: 10 AN: 152332 Hom.: 0 Cov.: 34 AF XY: 0.0000268 AC XY: 2 AN XY: 74496

African (AFR) AF: 0.0000241 AC: 1 AN: 41574

American (AMR) AF: 0.000131 AC: 2 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3472

East Asian (EAS) AF: 0.00 AC: 0 AN: 5190

South Asian (SAS) AF: 0.00 AC: 0 AN: 4832

European-Finnish (FIN) AF: 0.0000942 AC: 1 AN: 10616

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.0000882 AC: 6 AN: 68018

Other (OTH) AF: 0.00 AC: 0 AN: 2116

Alfa AF: 0.00 Hom.: 82

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.2
DANN	Benign	0.59
PhyloP100		-3.4
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs6712; hg19: chr22-50637922;