rs921351

chr10-109944957-T-C

Variant summary

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

The ENST00000369657.5(ADD3-AS1):n.137-2097A>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 0.233 in 152,206 control chromosomes in the GnomAD database, including 5,101 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 (5101 hom., cov: 33)
• Consequence: ADD3-AS1 ENST00000369657.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.144

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=-0.73).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.478 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.137-2097A>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.233 AC: 35477 AN: 152088 Hom.: 5083 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: 0.493

Gnomad FIN AF: 0.147

Gnomad MID AF: 0.236

Gnomad NFE AF: 0.157

Gnomad OTH AF: 0.224

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

GnomAD4 genome AF: 0.233 AC: 35536 AN: 152206 Hom.: 5101 Cov.: 33 AF XY: 0.238 AC XY: 17736 AN XY: 74424

Gnomad4 AFR AF: 0.364

Gnomad4 AMR AF: 0.153

Gnomad4 ASJ AF: 0.212

Gnomad4 EAS AF: 0.403

Gnomad4 SAS AF: 0.495

Gnomad4 FIN AF: 0.147

Gnomad4 NFE AF: 0.157

Gnomad4 OTH AF: 0.225

Alfa AF: 0.186 Hom.: 558

Bravo AF: 0.232

Asia WGS AF: 0.447 AC: 1554 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
Cadd	Benign	16
Dann	Benign	0.87

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs921351; hg19: chr10-111704715;