rs943887

Variant names:

• chr14-22546919-G-A
• rs943887

Your query was ambiguous. Multiple possible variants found:

• chr14-22546919-G-A
• chr14-22546919-G-C
• chr14-22546919-G-T

Variant summary

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

The variant allele was found at a frequency of 0.319 in 152,146 control chromosomes in the GnomAD database, including 7,956 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 0.32 (7956 hom., cov: 33)
• Consequence: TRA intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.715
• Publications: 0 publications found

Genes affected

TRA (HGNC:12027):

ACMG classification

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

• BP4: Computational evidence support a benign effect (Cadd=0.227).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.393 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TRA		n.22546919G>A		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.319 AC: 48483 AN: 152028 Hom.: 7946 Cov.: 33

Gnomad AFR AF: 0.231

Gnomad AMI AF: 0.357

Gnomad AMR AF: 0.399

Gnomad ASJ AF: 0.346

Gnomad EAS AF: 0.317

Gnomad SAS AF: 0.408

Gnomad FIN AF: 0.317

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.346

Gnomad OTH AF: 0.324

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

GnomAD4 genome AF: 0.319 AC: 48512 AN: 152146 Hom.: 7956 Cov.: 33 AF XY: 0.320 AC XY: 23770 AN XY: 74366

African (AFR) AF: 0.231 AC: 9569 AN: 41508

American (AMR) AF: 0.399 AC: 6099 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.346 AC: 1201 AN: 3472

East Asian (EAS) AF: 0.318 AC: 1642 AN: 5170

South Asian (SAS) AF: 0.408 AC: 1962 AN: 4812

European-Finnish (FIN) AF: 0.317 AC: 3362 AN: 10590

Middle Eastern (MID) AF: 0.429 AC: 126 AN: 294

European-Non Finnish (NFE) AF: 0.346 AC: 23532 AN: 67996

Other (OTH) AF: 0.328 AC: 693 AN: 2114

Alfa AF: 0.337 Hom.: 1796

Bravo AF: 0.318

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
CADD	Benign	0.23
PhyloP100		-0.71

Splicing

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

Other links and lift over

dbSNP: rs943887; hg19: -;