rs13212921

Variant names:

• chr6-27237643-C-T
• rs13212921
• unassigned_transcript_1004:c.2G>A

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000000000(TRI-AAT5-3):​c.2G>A​(p.Gly1Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0846 in 152,276 control chromosomes in the GnomAD database, including 645 homozygotes. In-silico tool predicts a benign outcome for this variant. 4/4 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.085 (645 hom., cov: 32)
• Consequence: TRI-AAT5-3 ENST00000000000 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.637
• Publications: 20 publications found

Genes affected

TRI-AAT5-3 (HGNC:34877):

ENSG00000294330 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.44).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.112 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TRI-AAT5-3	unassigned_transcript_1004	c.2G>A	p.Gly1Asp	missense_variant	Exon 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000294330	ENST00000722805.1	n.880+303G>A		intron_variant	Intron 1 of 1
ENSG00000294330	ENST00000722806.1	n.177-637G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0846 AC: 12880 AN: 152158 Hom.: 645 Cov.: 32

Gnomad AFR AF: 0.0740

Gnomad AMI AF: 0.175

Gnomad AMR AF: 0.0513

Gnomad ASJ AF: 0.0469

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0194

Gnomad FIN AF: 0.0648

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.114

Gnomad OTH AF: 0.0688

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0846 AC: 12885 AN: 152276 Hom.: 645 Cov.: 32 AF XY: 0.0799 AC XY: 5951 AN XY: 74458

African (AFR) AF: 0.0740 AC: 3075 AN: 41548

American (AMR) AF: 0.0512 AC: 784 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.0469 AC: 163 AN: 3472

East Asian (EAS) AF: 0.00 AC: 0 AN: 5184

South Asian (SAS) AF: 0.0190 AC: 92 AN: 4832

European-Finnish (FIN) AF: 0.0648 AC: 687 AN: 10606

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.114 AC: 7767 AN: 68010

Other (OTH) AF: 0.0676 AC: 143 AN: 2114

Alfa AF: 0.0983 Hom.: 1043

Bravo AF: 0.0825

Asia WGS AF: 0.0170 AC: 62 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.44
CADD	Benign	7.4
DANN	Benign	0.84
PhyloP100		0.64

Splicing

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

Other links and lift over

dbSNP: rs13212921; hg19: chr6-27205422;