rs3811321

Variant names:

• chr14-22013585-A-C
• rs3811321
• ENST00000553572.2:n.1676A>C

Your query was ambiguous. Multiple possible variants found:

• chr14-22013585-A-C
• chr14-22013585-A-G
• chr14-22013585-A-T

Variant summary

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

The ENST00000553572.2(ENSG00000258705):​n.1676A>C variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.0935 in 152,438 control chromosomes in the GnomAD database, including 991 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 0.094 (988 hom., cov: 28)
  • Exomes 𝑓: 0.077 (3 hom.)
• Consequence: ENSG00000258705 ENST00000553572.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.01
• Publications: 11 publications found

Genes affected

ENSG00000258705 (HGNC:):

TRA (HGNC:12027):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.66).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.189 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000553572.2. 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
	ENSG00000258705	ENST00000553572.2	TSL:6	n.1676A>C		non_coding_transcript_exon	Exon 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0934 AC: 14177 AN: 151752 Hom.: 978 Cov.: 28

Gnomad AFR AF: 0.192

Gnomad AMI AF: 0.0474

Gnomad AMR AF: 0.0471

Gnomad ASJ AF: 0.0836

Gnomad EAS AF: 0.0488

Gnomad SAS AF: 0.0796

Gnomad FIN AF: 0.0129

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.0624

Gnomad OTH AF: 0.0868

GnomAD4 exome AF: 0.0775 AC: 44 AN: 568 Hom.: 3 Cov.: 0 AF XY: 0.0806 AC XY: 25 AN XY: 310

African (AFR) AF: 0.167 AC: 4 AN: 24

American (AMR) AF: 0.00 AC: 0 AN: 2

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2

East Asian (EAS) AF: 0.00 AC: 0 AN: 6

South Asian (SAS) AF: 0.188 AC: 3 AN: 16

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 20

Middle Eastern (MID) AF: 0.0740 AC: 25 AN: 338

European-Non Finnish (NFE) AF: 0.0614 AC: 7 AN: 114

Other (OTH) AF: 0.109 AC: 5 AN: 46

GnomAD4 genome AF: 0.0936 AC: 14216 AN: 151870 Hom.: 988 Cov.: 28 AF XY: 0.0909 AC XY: 6750 AN XY: 74250

African (AFR) AF: 0.192 AC: 7949 AN: 41314

American (AMR) AF: 0.0470 AC: 717 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.0836 AC: 290 AN: 3470

East Asian (EAS) AF: 0.0491 AC: 254 AN: 5170

South Asian (SAS) AF: 0.0799 AC: 384 AN: 4806

European-Finnish (FIN) AF: 0.0129 AC: 137 AN: 10600

Middle Eastern (MID) AF: 0.0884 AC: 26 AN: 294

European-Non Finnish (NFE) AF: 0.0623 AC: 4236 AN: 67962

Other (OTH) AF: 0.0859 AC: 180 AN: 2096

Alfa AF: 0.0754 Hom.: 1139

Bravo AF: 0.0985

Asia WGS AF: 0.0650 AC: 226 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	7.8
DANN	Benign	0.30
PhyloP100		4.0

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: rs3811321;

hg19: chr14-22481824;