rs3862006

Variant names:

• chr10-109991006-G-A
• rs3862006
• ENST00000369655.4:n.335+14951C>T

Variant summary

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

The ENST00000369655.4(ADD3-AS1):​n.335+14951C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.206 in 152,108 control chromosomes in the GnomAD database, including 3,808 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 0.21 (3808 hom., cov: 32)
• Consequence: ADD3-AS1 ENST00000369655.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0620
• 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=-0.61).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.468 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ADD3-AS1	NR_038943.1	n.326+14951C>T		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ADD3-AS1	ENST00000369655.4	n.335+14951C>T		intron_variant	Intron 2 of 5	1
ADD3-AS1	ENST00000625954.4	n.335+14951C>T		intron_variant	Intron 2 of 4	3
ADD3-AS1	ENST00000627565.2	n.453+6443C>T		intron_variant	Intron 3 of 5	3

Frequencies

GnomAD3 genomes AF: 0.206 AC: 31336 AN: 151990 Hom.: 3802 Cov.: 32

Gnomad AFR AF: 0.280

Gnomad AMI AF: 0.0965

Gnomad AMR AF: 0.139

Gnomad ASJ AF: 0.213

Gnomad EAS AF: 0.392

Gnomad SAS AF: 0.482

Gnomad FIN AF: 0.147

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.153

Gnomad OTH AF: 0.201

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

GnomAD4 genome AF: 0.206 AC: 31370 AN: 152108 Hom.: 3808 Cov.: 32 AF XY: 0.212 AC XY: 15737 AN XY: 74364

African (AFR) AF: 0.280 AC: 11607 AN: 41448

American (AMR) AF: 0.139 AC: 2125 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.213 AC: 737 AN: 3468

East Asian (EAS) AF: 0.392 AC: 2029 AN: 5178

South Asian (SAS) AF: 0.484 AC: 2336 AN: 4826

European-Finnish (FIN) AF: 0.147 AC: 1553 AN: 10584

Middle Eastern (MID) AF: 0.228 AC: 67 AN: 294

European-Non Finnish (NFE) AF: 0.153 AC: 10401 AN: 68008

Other (OTH) AF: 0.202 AC: 427 AN: 2110

Alfa AF: 0.166 Hom.: 607

Bravo AF: 0.201

Asia WGS AF: 0.432 AC: 1504 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.61
CADD	Benign	3.3
DANN	Benign	0.76
PhyloP100		0.062

Splicing

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

Other links and lift over

dbSNP: rs3862006; hg19: chr10-111750764;