10-109947740-A-G

Position:

• chr10-109947740-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_038943.1(ADD3-AS1):​n.463-464T>C variant causes a intron, non coding transcript 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 NR_038943.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.92

Genes affected

ADD3-AS1 (HGNC:48682): (ADD3 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ADD3-AS1	NR_038943.1	n.463-464T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ADD3-AS1	ENST00000627565.2	n.590-464T>C		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR AF: 0.333

Gnomad4 AMR AF: 0.148

Gnomad4 ASJ AF: 0.212

Gnomad4 EAS AF: 0.403

Gnomad4 SAS AF: 0.493

Gnomad4 FIN AF: 0.146

Gnomad4 NFE AF: 0.157

Gnomad4 OTH AF: 0.219

Alfa AF: 0.187 Hom.: 1960

Bravo AF: 0.221

Asia WGS AF: 0.441 AC: 1533 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	15
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs921348; hg19: chr10-111707498;