10-109956909-G-C

Variant names:

• chr10-109956909-G-C
• rs731793
• ENST00000369655.4:n.336-3018C>G

Variant summary

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

The ENST00000631276.2(ADD3-AS1):​n.1003C>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.243 in 152,100 control chromosomes in the GnomAD database, including 5,634 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 0.24 (5634 hom., cov: 32)
  • Exomes 𝑓: 0.10 (0 hom.)
• Consequence: ADD3-AS1 ENST00000631276.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.72
• Publications: 3 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=-0.56).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.497 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000631276.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ADD3-AS1	NR_038943.1		n.327-3018C>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ADD3-AS1	ENST00000369655.4	TSL:1	n.336-3018C>G		intron	N/A
	ADD3-AS1	ENST00000631276.2	TSL:2	n.1003C>G		non_coding_transcript_exon	Exon 1 of 3
	ADD3-AS1	ENST00000625954.4	TSL:3	n.336-3018C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.243 AC: 36872 AN: 151960 Hom.: 5611 Cov.: 32

Gnomad AFR AF: 0.394

Gnomad AMI AF: 0.0965

Gnomad AMR AF: 0.156

Gnomad ASJ AF: 0.213

Gnomad EAS AF: 0.403

Gnomad SAS AF: 0.513

Gnomad FIN AF: 0.147

Gnomad MID AF: 0.242

Gnomad NFE AF: 0.157

Gnomad OTH AF: 0.229

GnomAD4 exome AF: 0.100 AC: 2 AN: 20 Hom.: 0 Cov.: 0 AF XY: 0.0625 AC XY: 1 AN XY: 16

African (AFR) AF: 0.500 AC: 1 AN: 2

American (AMR) AF: 0.00 AC: 0 AN: 2

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.00 AC: 0 AN: 2

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2

European-Non Finnish (NFE) AF: 0.0833 AC: 1 AN: 12

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.243 AC: 36946 AN: 152080 Hom.: 5634 Cov.: 32 AF XY: 0.248 AC XY: 18412 AN XY: 74374

African (AFR) AF: 0.395 AC: 16359 AN: 41414

American (AMR) AF: 0.156 AC: 2380 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.213 AC: 738 AN: 3472

East Asian (EAS) AF: 0.403 AC: 2084 AN: 5168

South Asian (SAS) AF: 0.514 AC: 2477 AN: 4818

European-Finnish (FIN) AF: 0.147 AC: 1555 AN: 10602

Middle Eastern (MID) AF: 0.241 AC: 71 AN: 294

European-Non Finnish (NFE) AF: 0.157 AC: 10707 AN: 67998

Other (OTH) AF: 0.230 AC: 487 AN: 2114

Alfa AF: 0.0870 Hom.: 134

Bravo AF: 0.243

Asia WGS AF: 0.456 AC: 1587 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.56
CADD	Benign	18
DANN	Benign	0.75
PhyloP100		1.7

Splicing

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

Other links and lift over

dbSNP: rs731793; hg19: chr10-111716667; COSMIC: COSV63734329;