rs3117099

Variant names:

• chr6-32390493-G-A
• rs3117099
• ENST00000642577.1:n.448G>A

Your query was ambiguous. Multiple possible variants found:

• chr6-32390493-G-A
• chr6-32390493-G-C
• chr6-32390493-G-T

Variant summary

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

The ENST00000642577.1(TSBP1-AS1):​n.448G>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 0.277 in 154,250 control chromosomes in the GnomAD database, including 6,341 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 0.28 (6203 hom., cov: 32)
  • Exomes 𝑓: 0.22 (138 hom.)
• Consequence: TSBP1-AS1 ENST00000642577.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0320
• Publications: 45 publications found

Genes affected

TSBP1-AS1 (HGNC:39756): (TSBP1 and BTNL2 antisense RNA 1)

HCG23 (HGNC:19713): (HLA complex group 23)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.403 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000642577.1. 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
	TSBP1-AS1	NR_136245.1		n.303-14961G>A		intron	N/A
	HCG23	NR_044996.1		n.-17G>A		upstream_gene	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TSBP1-AS1	ENST00000642577.1		n.448G>A		non_coding_transcript_exon	Exon 3 of 6
	TSBP1-AS1	ENST00000644884.2		n.1148G>A		non_coding_transcript_exon	Exon 4 of 4
	TSBP1-AS1	ENST00000645134.1		n.367G>A		non_coding_transcript_exon	Exon 2 of 5

Frequencies

GnomAD3 genomes AF: 0.279 AC: 41566 AN: 148974 Hom.: 6192 Cov.: 32

Gnomad AFR AF: 0.392

Gnomad AMI AF: 0.139

Gnomad AMR AF: 0.230

Gnomad ASJ AF: 0.296

Gnomad EAS AF: 0.417

Gnomad SAS AF: 0.268

Gnomad FIN AF: 0.266

Gnomad MID AF: 0.173

Gnomad NFE AF: 0.215

Gnomad OTH AF: 0.283

GnomAD4 exome AF: 0.222 AC: 1144 AN: 5156 Hom.: 138 Cov.: 0 AF XY: 0.220 AC XY: 610 AN XY: 2776

African (AFR) AF: 0.349 AC: 30 AN: 86

American (AMR) AF: 0.236 AC: 25 AN: 106

Ashkenazi Jewish (ASJ) AF: 0.227 AC: 35 AN: 154

East Asian (EAS) AF: 0.396 AC: 259 AN: 654

South Asian (SAS) AF: 0.205 AC: 9 AN: 44

European-Finnish (FIN) AF: 0.201 AC: 136 AN: 676

Middle Eastern (MID) AF: 0.192 AC: 5 AN: 26

European-Non Finnish (NFE) AF: 0.187 AC: 580 AN: 3104

Other (OTH) AF: 0.212 AC: 65 AN: 306

GnomAD4 genome AF: 0.279 AC: 41612 AN: 149094 Hom.: 6203 Cov.: 32 AF XY: 0.278 AC XY: 20242 AN XY: 72782

African (AFR) AF: 0.392 AC: 15903 AN: 40582

American (AMR) AF: 0.231 AC: 3474 AN: 15064

Ashkenazi Jewish (ASJ) AF: 0.296 AC: 1024 AN: 3458

East Asian (EAS) AF: 0.417 AC: 2153 AN: 5160

South Asian (SAS) AF: 0.268 AC: 1279 AN: 4778

European-Finnish (FIN) AF: 0.266 AC: 2638 AN: 9910

Middle Eastern (MID) AF: 0.176 AC: 51 AN: 290

European-Non Finnish (NFE) AF: 0.215 AC: 14381 AN: 66896

Other (OTH) AF: 0.282 AC: 587 AN: 2078

Alfa AF: 0.242 Hom.: 15075

Bravo AF: 0.276

Asia WGS AF: 0.371 AC: 1285 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.7
DANN	Benign	0.42
PhyloP100		-0.032
Mutation Taster		=100/0	polymorphism

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: rs3117099;

hg19: chr6-32358270;