chr10-109941164-C-T

Position:

• chr10-109941164-C-T

Variant summary

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

The ENST00000369657.5(ADD3-AS1):​n.822G>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 0.232 in 155,312 control chromosomes in the GnomAD database, including 5,161 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 0.23 (5082 hom., cov: 33)
  • Exomes 𝑓: 0.17 (79 hom.)
• Consequence: ADD3-AS1 ENST00000369657.5 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.864

Genes affected

ADD3-AS1 (HGNC:48682): (ADD3 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.477 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ADD3-AS1	ENST00000369657.5	n.822G>A		non_coding_transcript_exon_variant	3/3	5

Frequencies

GnomAD3 genomes AF: 0.233 AC: 35446 AN: 151986 Hom.: 5066 Cov.: 33

Gnomad AFR AF: 0.364

Gnomad AMI AF: 0.0965

Gnomad AMR AF: 0.153

Gnomad ASJ AF: 0.212

Gnomad EAS AF: 0.403

Gnomad SAS AF: 0.492

Gnomad FIN AF: 0.147

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.157

Gnomad OTH AF: 0.224

GnomAD4 exome AF: 0.166 AC: 534 AN: 3208 Hom.: 79 Cov.: 0 AF XY: 0.177 AC XY: 295 AN XY: 1664

Gnomad4 AFR exome AF: 0.360

Gnomad4 AMR exome AF: 0.0835

Gnomad4 ASJ exome AF: 0.184

Gnomad4 EAS exome AF: 0.321

Gnomad4 SAS exome AF: 0.438

Gnomad4 FIN exome AF: 0.154

Gnomad4 NFE exome AF: 0.132

Gnomad4 OTH exome AF: 0.200

GnomAD4 genome AF: 0.233 AC: 35501 AN: 152104 Hom.: 5082 Cov.: 33 AF XY: 0.238 AC XY: 17723 AN XY: 74376

Gnomad4 AFR AF: 0.364

Gnomad4 AMR AF: 0.153

Gnomad4 ASJ AF: 0.212

Gnomad4 EAS AF: 0.403

Gnomad4 SAS AF: 0.494

Gnomad4 FIN AF: 0.147

Gnomad4 NFE AF: 0.157

Gnomad4 OTH AF: 0.225

Alfa AF: 0.186 Hom.: 559

Bravo AF: 0.232

Asia WGS AF: 0.445 AC: 1547 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	1.1
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11194926; hg19: chr10-111700922;