10-109978693-T-C

Variant names:

• chr10-109978693-T-C
• rs9630101
• ENST00000369655.4:n.336-24802A>G

Variant summary

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

The ENST00000369655.4(ADD3-AS1):​n.336-24802A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.25 in 152,038 control chromosomes in the GnomAD database, including 6,061 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 0.25 (6061 hom., cov: 32)
• Consequence: ADD3-AS1 ENST00000369655.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.01
• Publications: 7 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=-0.67).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.496 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000369655.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ADD3-AS1	NR_038943.1		n.327-24802A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ADD3-AS1	ENST00000369655.4	TSL:1	n.336-24802A>G		intron	N/A
	ADD3-AS1	ENST00000625954.4	TSL:3	n.336-24802A>G		intron	N/A
	ADD3-AS1	ENST00000627565.2	TSL:3	n.453+18756A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.250 AC: 37929 AN: 151918 Hom.: 6035 Cov.: 32

Gnomad AFR AF: 0.418

Gnomad AMI AF: 0.0965

Gnomad AMR AF: 0.160

Gnomad ASJ AF: 0.213

Gnomad EAS AF: 0.402

Gnomad SAS AF: 0.511

Gnomad FIN AF: 0.147

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.158

Gnomad OTH AF: 0.237

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

GnomAD4 genome AF: 0.250 AC: 38009 AN: 152038 Hom.: 6061 Cov.: 32 AF XY: 0.254 AC XY: 18876 AN XY: 74348

African (AFR) AF: 0.418 AC: 17316 AN: 41404

American (AMR) AF: 0.160 AC: 2448 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.213 AC: 738 AN: 3470

East Asian (EAS) AF: 0.403 AC: 2081 AN: 5166

South Asian (SAS) AF: 0.513 AC: 2468 AN: 4814

European-Finnish (FIN) AF: 0.147 AC: 1553 AN: 10576

Middle Eastern (MID) AF: 0.255 AC: 75 AN: 294

European-Non Finnish (NFE) AF: 0.158 AC: 10740 AN: 68000

Other (OTH) AF: 0.238 AC: 502 AN: 2112

Alfa AF: 0.194 Hom.: 9416

Bravo AF: 0.251

Asia WGS AF: 0.458 AC: 1593 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	13
DANN	Benign	0.63
PhyloP100		1.0

Splicing

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

Other links and lift over

dbSNP: rs9630101; hg19: chr10-111738451;