rs3117098

chr6-32390736-G-Achr6-32390736-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_044996.1(HCG23):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: HCG23 NR_044996.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.567

Genes affected

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

HCG23 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
HCG23	NR_044996.1	n.227G>A		non_coding_transcript_exon_variant	1/3
TSBP1-AS1	NR_136245.1	n.303-14718G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TSBP1-AS1	ENST00000645134.1	n.610G>A		non_coding_transcript_exon_variant	2/5

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

Gnomad4 ASJ exome AF: 0.00

Gnomad4 FIN exome AF: 0.500

Gnomad4 NFE exome AF: 0.500

Gnomad4 OTH exome AF: 0.500

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

Gnomad4 AFR AF: 0.772

Gnomad4 AMR AF: 0.691

Gnomad4 ASJ AF: 0.695

Gnomad4 EAS AF: 0.734

Gnomad4 SAS AF: 0.710

Gnomad4 FIN AF: 0.755

Gnomad4 NFE AF: 0.686

Gnomad4 OTH AF: 0.717

Alfa AF: 0.686 Hom.: 48891

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3117098; hg19: chr6-32358513;