rs921351

Variant names:

• chr10-109944957-T-C
• rs921351
• ENST00000369657.5:n.137-2097A>G

Variant summary

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

The ENST00000369657.5(ADD3-AS1):​n.137-2097A>G variant causes a intron 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.144
• Publications: 4 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ADD3-AS1	ENST00000369657.5	n.137-2097A>G		intron_variant	Intron 1 of 2	5
ADD3-AS1	ENST00000767402.1	n.314-14867A>G		intron_variant	Intron 2 of 2
ADD3-AS1	ENST00000767403.1	n.219+8799A>G		intron_variant	Intron 2 of 2
ADD3-AS1	ENST00000767406.1	n.152+8799A>G		intron_variant	Intron 1 of 1

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

African (AFR) AF: 0.364 AC: 15126 AN: 41502

American (AMR) AF: 0.153 AC: 2336 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.212 AC: 735 AN: 3466

East Asian (EAS) AF: 0.403 AC: 2091 AN: 5184

South Asian (SAS) AF: 0.495 AC: 2386 AN: 4824

European-Finnish (FIN) AF: 0.147 AC: 1563 AN: 10608

Middle Eastern (MID) AF: 0.229 AC: 67 AN: 292

European-Non Finnish (NFE) AF: 0.157 AC: 10669 AN: 68006

Other (OTH) AF: 0.225 AC: 475 AN: 2108

Alfa AF: 0.209 Hom.: 1409

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
PhyloP100		0.14
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs921351; hg19: chr10-111704715;