ENST00000369655.4:n.336-22101G>A

Variant names:

• chr10-109975992-C-T
• rs17095355
• ENST00000369655.4:n.336-22101G>A

Variant summary

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

The ENST00000369655.4(ADD3-AS1):​n.336-22101G>A variant causes a intron 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 ENST00000369655.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.16
• Publications: 48 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=-0.79).
• 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 rank	MANE	Protein	UniProt
ADD3-AS1	NR_038943.1	n.327-22101G>A		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ADD3-AS1	ENST00000369655.4	n.336-22101G>A		intron_variant	Intron 2 of 5	1
ADD3-AS1	ENST00000625954.4	n.336-22101G>A		intron_variant	Intron 2 of 4	3
ADD3-AS1	ENST00000627565.2	n.453+21457G>A		intron_variant	Intron 3 of 5	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

African (AFR) AF: 0.334 AC: 13842 AN: 41420

American (AMR) AF: 0.147 AC: 2250 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.211 AC: 731 AN: 3470

East Asian (EAS) AF: 0.402 AC: 2076 AN: 5162

South Asian (SAS) AF: 0.488 AC: 2349 AN: 4812

European-Finnish (FIN) AF: 0.147 AC: 1556 AN: 10550

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.156 AC: 10619 AN: 67984

Other (OTH) AF: 0.218 AC: 459 AN: 2110

Alfa AF: 0.186 Hom.: 9467

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
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs17095355; hg19: chr10-111735750;