chr10-109947740-A-G

Variant names:

• chr10-109947740-A-G
• rs921348
• ENST00000369655.4:n.594-464T>C

Variant summary

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

The ENST00000369655.4(ADD3-AS1):​n.594-464T>C 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 152,072 control chromosomes in the GnomAD database, including 4,605 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 (4605 hom., cov: 32)
• Consequence: ADD3-AS1 ENST00000369655.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.92
• 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=-0.64).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.476 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.463-464T>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ADD3-AS1	ENST00000369655.4	TSL:1	n.594-464T>C		intron	N/A
	ADD3-AS1	ENST00000369657.5	TSL:5	n.137-4880T>C		intron	N/A
	ADD3-AS1	ENST00000625954.4	TSL:3	n.472-464T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.224 AC: 34046 AN: 151954 Hom.: 4597 Cov.: 32

Gnomad AFR AF: 0.334

Gnomad AMI AF: 0.0967

Gnomad AMR AF: 0.148

Gnomad ASJ AF: 0.212

Gnomad EAS AF: 0.403

Gnomad SAS AF: 0.491

Gnomad FIN AF: 0.146

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.157

Gnomad OTH AF: 0.217

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

GnomAD4 genome AF: 0.224 AC: 34084 AN: 152072 Hom.: 4605 Cov.: 32 AF XY: 0.229 AC XY: 17059 AN XY: 74352

African (AFR) AF: 0.333 AC: 13812 AN: 41420

American (AMR) AF: 0.148 AC: 2255 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.212 AC: 734 AN: 3466

East Asian (EAS) AF: 0.403 AC: 2086 AN: 5172

South Asian (SAS) AF: 0.493 AC: 2375 AN: 4822

European-Finnish (FIN) AF: 0.146 AC: 1550 AN: 10590

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

European-Non Finnish (NFE) AF: 0.157 AC: 10654 AN: 67996

Other (OTH) AF: 0.219 AC: 462 AN: 2114

Alfa AF: 0.189 Hom.: 2243

Bravo AF: 0.221

Asia WGS AF: 0.441 AC: 1533 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	15
DANN	Benign	0.65
PhyloP100		1.9
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs921348; hg19: chr10-111707498;