rs12571674

chr10-109957850-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.327-3959T>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 0.148 in 152,138 control chromosomes in the GnomAD database, including 2,070 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 0.15 (2070 hom., cov: 32)
  • Exomes 𝑓: 0.50 (0 hom.)
• Consequence: ADD3-AS1 NR_038943.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.600

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=-0.75).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.382 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ADD3-AS1	NR_038943.1	n.327-3959T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ADD3-AS1	ENST00000369655.3	n.85-3959T>C		intron_variant, non_coding_transcript_variant		1
ADD3-AS1	ENST00000627565.2	n.454-3959T>C		intron_variant, non_coding_transcript_variant		3
ADD3-AS1	ENST00000631276.2	n.62T>C		non_coding_transcript_exon_variant	1/3	2
ADD3-AS1	ENST00000625954.3	n.310-3959T>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.148 AC: 22431 AN: 152018 Hom.: 2071 Cov.: 32

Gnomad AFR AF: 0.107

Gnomad AMI AF: 0.0965

Gnomad AMR AF: 0.117

Gnomad ASJ AF: 0.189

Gnomad EAS AF: 0.396

Gnomad SAS AF: 0.394

Gnomad FIN AF: 0.123

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.145

Gnomad OTH AF: 0.150

GnomAD4 exome AF: 0.500 AC: 1 AN: 2 Hom.: 0 Cov.: 0 AF XY: 0.500 AC XY: 1 AN XY: 2

Gnomad4 NFE exome AF: 0.500

GnomAD4 genome AF: 0.148 AC: 22442 AN: 152136 Hom.: 2070 Cov.: 32 AF XY: 0.152 AC XY: 11329 AN XY: 74384

Gnomad4 AFR AF: 0.107

Gnomad4 AMR AF: 0.117

Gnomad4 ASJ AF: 0.189

Gnomad4 EAS AF: 0.397

Gnomad4 SAS AF: 0.395

Gnomad4 FIN AF: 0.123

Gnomad4 NFE AF: 0.145

Gnomad4 OTH AF: 0.153

Alfa AF: 0.135 Hom.: 277

Bravo AF: 0.140

Asia WGS AF: 0.390 AC: 1357 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
Cadd	Benign	3.2
Dann	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12571674; hg19: chr10-111717608; COSMIC: COSV63734502;