rs17095355

chr10-109975992-C-T

Variant summary

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

The NR_038943.1(ADD3-AS1):n.327-22101G>A 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 0.224 in 151,984 control chromosomes in the GnomAD database, including 4,602 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 0.22 (4602 hom., cov: 32)
• Consequence: ADD3-AS1 NR_038943.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.16

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=-0.79).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.472 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ADD3-AS1	NR_038943.1	n.327-22101G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ADD3-AS1	ENST00000369655.3	n.85-22101G>A		intron_variant, non_coding_transcript_variant		1
ADD3-AS1	ENST00000627565.2	n.453+21457G>A		intron_variant, non_coding_transcript_variant		3
ADD3-AS1	ENST00000625954.3	n.310-22101G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.224 AC: 33999 AN: 151866 Hom.: 4595 Cov.: 32

Gnomad AFR AF: 0.334

Gnomad AMI AF: 0.0965

Gnomad AMR AF: 0.148

Gnomad ASJ AF: 0.211

Gnomad EAS AF: 0.402

Gnomad SAS AF: 0.487

Gnomad FIN AF: 0.147

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.156

Gnomad OTH AF: 0.216

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

GnomAD4 genome AF: 0.224 AC: 34038 AN: 151984 Hom.: 4602 Cov.: 32 AF XY: 0.229 AC XY: 17027 AN XY: 74270

Gnomad4 AFR AF: 0.334

Gnomad4 AMR AF: 0.147

Gnomad4 ASJ AF: 0.211

Gnomad4 EAS AF: 0.402

Gnomad4 SAS AF: 0.488

Gnomad4 FIN AF: 0.147

Gnomad4 NFE AF: 0.156

Gnomad4 OTH AF: 0.218

Alfa AF: 0.177 Hom.: 3428

Bravo AF: 0.221

Asia WGS AF: 0.438 AC: 1524 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
Cadd	Benign	0.56
Dann	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17095355; hg19: chr10-111735750;