rs3862006

Positions:

• chr10-109991006-G-A

Variant summary

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

The NR_038943.1(ADD3-AS1):​n.326+14951C>T 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 0.206 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 NR_038943.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0620

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=-0.61).
• 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/exons	MANE	UniProt
ADD3-AS1	NR_038943.1	n.326+14951C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ADD3-AS1	ENST00000369655.3	n.84+14951C>T		intron_variant, non_coding_transcript_variant		1
ADD3-AS1	ENST00000627565.2	n.453+6443C>T		intron_variant, non_coding_transcript_variant		3
ADD3-AS1	ENST00000625954.3	n.309+14951C>T		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.280

Gnomad4 AMR AF: 0.139

Gnomad4 ASJ AF: 0.213

Gnomad4 EAS AF: 0.392

Gnomad4 SAS AF: 0.484

Gnomad4 FIN AF: 0.147

Gnomad4 NFE AF: 0.153

Gnomad4 OTH AF: 0.202

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3862006; hg19: chr10-111750764;