rs17299841

Variant names:

• chr6-127700658-A-C
• rs17299841
• XM_047418764.1:c.*9327T>G

Your query was ambiguous. Multiple possible variants found:

• chr6-127700658-A-C
• chr6-127700658-A-G

Variant summary

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

The XM_047418764.1(THEMIS):​c.*9327T>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.064 in 152,110 control chromosomes in the GnomAD database, including 415 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 0.064 (415 hom., cov: 32)
• Consequence: THEMIS XM_047418764.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.638
• Publications: 8 publications found

Genes affected

THEMIS (HGNC:21569): (thymocyte selection associated) This gene encodes a protein that plays a regulatory role in both positive and negative T-cell selection during late thymocyte development. The protein functions through T-cell antigen receptor signaling, and is necessary for proper lineage commitment and maturation of T-cells. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Sep 2009]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.09 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
THEMIS	XM_047418764.1	c.*9327T>G		3_prime_UTR_variant	Exon 7 of 8		XP_047274720.1
THEMIS	XM_047418766.1	c.*9327T>G		3_prime_UTR_variant	Exon 7 of 8		XP_047274722.1

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0641 AC: 9750 AN: 151994 Hom.: 416 Cov.: 32

Gnomad AFR AF: 0.0211

Gnomad AMI AF: 0.111

Gnomad AMR AF: 0.0591

Gnomad ASJ AF: 0.0649

Gnomad EAS AF: 0.00115

Gnomad SAS AF: 0.0567

Gnomad FIN AF: 0.0955

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.0919

Gnomad OTH AF: 0.0522

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

GnomAD4 genome AF: 0.0640 AC: 9741 AN: 152110 Hom.: 415 Cov.: 32 AF XY: 0.0615 AC XY: 4570 AN XY: 74366

African (AFR) AF: 0.0211 AC: 877 AN: 41568

American (AMR) AF: 0.0587 AC: 897 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0649 AC: 225 AN: 3466

East Asian (EAS) AF: 0.00116 AC: 6 AN: 5188

South Asian (SAS) AF: 0.0557 AC: 269 AN: 4828

European-Finnish (FIN) AF: 0.0955 AC: 1012 AN: 10592

Middle Eastern (MID) AF: 0.0170 AC: 5 AN: 294

European-Non Finnish (NFE) AF: 0.0919 AC: 6239 AN: 67874

Other (OTH) AF: 0.0521 AC: 110 AN: 2112

Alfa AF: 0.0792 Hom.: 1726

Bravo AF: 0.0607

Asia WGS AF: 0.0320 AC: 112 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	11
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: rs17299841; hg19: chr6-128021803;