10-109951059-T-C

Position:

• chr10-109951059-T-C

Variant summary

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

The NR_038943.1(ADD3-AS1):​n.462+2697A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.244 in 152,138 control chromosomes in the GnomAD database, including 5,658 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 0.24 (5658 hom., cov: 32)
• Consequence: ADD3-AS1 NR_038943.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.23

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=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.497 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ADD3-AS1	NR_038943.1	n.462+2697A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ADD3-AS1	ENST00000627565.2	n.589+2697A>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.243 AC: 36998 AN: 152020 Hom.: 5636 Cov.: 32

Gnomad AFR AF: 0.395

Gnomad AMI AF: 0.0965

Gnomad AMR AF: 0.157

Gnomad ASJ AF: 0.213

Gnomad EAS AF: 0.403

Gnomad SAS AF: 0.513

Gnomad FIN AF: 0.146

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.158

Gnomad OTH AF: 0.232

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

GnomAD4 genome AF: 0.244 AC: 37070 AN: 152138 Hom.: 5658 Cov.: 32 AF XY: 0.248 AC XY: 18469 AN XY: 74384

Gnomad4 AFR AF: 0.396

Gnomad4 AMR AF: 0.157

Gnomad4 ASJ AF: 0.213

Gnomad4 EAS AF: 0.403

Gnomad4 SAS AF: 0.514

Gnomad4 FIN AF: 0.146

Gnomad4 NFE AF: 0.158

Gnomad4 OTH AF: 0.232

Alfa AF: 0.198 Hom.: 729

Bravo AF: 0.243

Asia WGS AF: 0.454 AC: 1579 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.0
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7080576; hg19: chr10-111710817;