rs3117098

Variant names:

• chr6-32390736-G-A
• rs3117098
• ENST00000426643.1:n.227G>A

Your query was ambiguous. Multiple possible variants found:

• chr6-32390736-G-A
• chr6-32390736-G-C
• chr6-32390736-G-T

Variant summary

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

The ENST00000426643.1(TSBP1-AS1):​n.227G>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 0.718 in 152,090 control chromosomes in the GnomAD database, including 39,385 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 0.72 (39385 hom., cov: 32)
  • Exomes 𝑓: 0.40 (0 hom.)
• Consequence: TSBP1-AS1 ENST00000426643.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.567
• Publications: 76 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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.765 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HCG23	NR_044996.1	n.227G>A		non_coding_transcript_exon_variant	Exon 1 of 3
TSBP1-AS1	NR_136245.1	n.303-14718G>A		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TSBP1-AS1	ENST00000426643.1	n.227G>A		non_coding_transcript_exon_variant	Exon 1 of 3	3
TSBP1-AS1	ENST00000642577.1	n.691G>A		non_coding_transcript_exon_variant	Exon 3 of 6
TSBP1-AS1	ENST00000644884.2	n.1391G>A		non_coding_transcript_exon_variant	Exon 4 of 4

Frequencies

GnomAD3 genomes AF: 0.718 AC: 109154 AN: 151962 Hom.: 39362 Cov.: 32

Gnomad AFR AF: 0.772

Gnomad AMI AF: 0.777

Gnomad AMR AF: 0.691

Gnomad ASJ AF: 0.695

Gnomad EAS AF: 0.734

Gnomad SAS AF: 0.711

Gnomad FIN AF: 0.755

Gnomad MID AF: 0.567

Gnomad NFE AF: 0.686

Gnomad OTH AF: 0.723

GnomAD4 exome AF: 0.400 AC: 4 AN: 10 Hom.: 0 Cov.: 0 AF XY: 0.333 AC XY: 2 AN XY: 6

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

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

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.500 AC: 1 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.500 AC: 2 AN: 4

Other (OTH) AF: 0.500 AC: 1 AN: 2

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0.0206134), which strongly suggests a high chance of mosaicism in these individuals.

GnomAD4 genome AF: 0.718 AC: 109224 AN: 152080 Hom.: 39385 Cov.: 32 AF XY: 0.717 AC XY: 53317 AN XY: 74328

African (AFR) AF: 0.772 AC: 32007 AN: 41478

American (AMR) AF: 0.691 AC: 10570 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.695 AC: 2414 AN: 3472

East Asian (EAS) AF: 0.734 AC: 3799 AN: 5174

South Asian (SAS) AF: 0.710 AC: 3421 AN: 4816

European-Finnish (FIN) AF: 0.755 AC: 7963 AN: 10552

Middle Eastern (MID) AF: 0.558 AC: 163 AN: 292

European-Non Finnish (NFE) AF: 0.686 AC: 46664 AN: 67986

Other (OTH) AF: 0.717 AC: 1514 AN: 2112

Alfa AF: 0.700 Hom.: 144935

Bravo AF: 0.721

Asia WGS AF: 0.720 AC: 2505 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.5
DANN	Benign	0.52
PhyloP100		-0.57

Splicing

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

Other links and lift over

dbSNP: rs3117098; hg19: chr6-32358513;