10-109941164-C-T

Variant names:

• chr10-109941164-C-T
• rs11194926
• ENST00000369657.5:n.822G>A

Variant summary

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

The ENST00000369657.5(ADD3-AS1):​n.822G>A 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 0.232 in 155,312 control chromosomes in the GnomAD database, including 5,161 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 0.23 (5082 hom., cov: 33)
  • Exomes 𝑓: 0.17 (79 hom.)
• Consequence: ADD3-AS1 ENST00000369657.5 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.864
• 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=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.477 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000369657.5. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ADD3-AS1	ENST00000369657.5	TSL:5	n.822G>A		non_coding_transcript_exon	Exon 3 of 3
	ADD3-AS1	ENST00000767402.1		n.314-11074G>A		intron	N/A
	ADD3-AS1	ENST00000767403.1		n.220-11074G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.233 AC: 35446 AN: 151986 Hom.: 5066 Cov.: 33

Gnomad AFR AF: 0.364

Gnomad AMI AF: 0.0965

Gnomad AMR AF: 0.153

Gnomad ASJ AF: 0.212

Gnomad EAS AF: 0.403

Gnomad SAS AF: 0.492

Gnomad FIN AF: 0.147

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.157

Gnomad OTH AF: 0.224

GnomAD4 exome AF: 0.166 AC: 534 AN: 3208 Hom.: 79 Cov.: 0 AF XY: 0.177 AC XY: 295 AN XY: 1664

African (AFR) AF: 0.360 AC: 31 AN: 86

American (AMR) AF: 0.0835 AC: 67 AN: 802

Ashkenazi Jewish (ASJ) AF: 0.184 AC: 7 AN: 38

East Asian (EAS) AF: 0.321 AC: 70 AN: 218

South Asian (SAS) AF: 0.438 AC: 112 AN: 256

European-Finnish (FIN) AF: 0.154 AC: 4 AN: 26

Middle Eastern (MID) AF: 0.500 AC: 1 AN: 2

European-Non Finnish (NFE) AF: 0.132 AC: 222 AN: 1680

Other (OTH) AF: 0.200 AC: 20 AN: 100

GnomAD4 genome AF: 0.233 AC: 35501 AN: 152104 Hom.: 5082 Cov.: 33 AF XY: 0.238 AC XY: 17723 AN XY: 74376

African (AFR) AF: 0.364 AC: 15101 AN: 41458

American (AMR) AF: 0.153 AC: 2334 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.212 AC: 737 AN: 3470

East Asian (EAS) AF: 0.403 AC: 2088 AN: 5182

South Asian (SAS) AF: 0.494 AC: 2382 AN: 4822

European-Finnish (FIN) AF: 0.147 AC: 1556 AN: 10570

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

European-Non Finnish (NFE) AF: 0.157 AC: 10673 AN: 67996

Other (OTH) AF: 0.225 AC: 474 AN: 2110

Alfa AF: 0.192 Hom.: 619

Bravo AF: 0.232

Asia WGS AF: 0.445 AC: 1547 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.1
DANN	Benign	0.76
PhyloP100		-0.86

Splicing

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

Other links and lift over

dbSNP: rs11194926; hg19: chr10-111700922;