rs734165

Variant names:

• chr10-109938031-C-T
• rs734165
• ENST00000767402.1:n.314-7941G>A

Variant summary

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

The ENST00000767402.1(ADD3-AS1):​n.314-7941G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.148 in 152,032 control chromosomes in the GnomAD database, including 2,067 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 (2067 hom., cov: 32)
• Consequence: ADD3-AS1 ENST00000767402.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.401
• Publications: 5 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=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.381 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000767402.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ADD3-AS1	ENST00000767402.1		n.314-7941G>A		intron	N/A
	ADD3-AS1	ENST00000767403.1		n.220-7941G>A		intron	N/A
	ADD3-AS1	ENST00000767406.1		n.153-7941G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.148 AC: 22473 AN: 151914 Hom.: 2068 Cov.: 32

Gnomad AFR AF: 0.107

Gnomad AMI AF: 0.0967

Gnomad AMR AF: 0.119

Gnomad ASJ AF: 0.188

Gnomad EAS AF: 0.395

Gnomad SAS AF: 0.391

Gnomad FIN AF: 0.123

Gnomad MID AF: 0.169

Gnomad NFE AF: 0.145

Gnomad OTH AF: 0.152

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

GnomAD4 genome AF: 0.148 AC: 22484 AN: 152032 Hom.: 2067 Cov.: 32 AF XY: 0.153 AC XY: 11333 AN XY: 74310

African (AFR) AF: 0.107 AC: 4445 AN: 41472

American (AMR) AF: 0.118 AC: 1810 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.188 AC: 653 AN: 3466

East Asian (EAS) AF: 0.395 AC: 2039 AN: 5164

South Asian (SAS) AF: 0.392 AC: 1888 AN: 4816

European-Finnish (FIN) AF: 0.123 AC: 1299 AN: 10534

Middle Eastern (MID) AF: 0.168 AC: 49 AN: 292

European-Non Finnish (NFE) AF: 0.145 AC: 9889 AN: 67992

Other (OTH) AF: 0.154 AC: 324 AN: 2102

Alfa AF: 0.137 Hom.: 287

Bravo AF: 0.141

Asia WGS AF: 0.388 AC: 1352 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.1
DANN	Benign	0.76
PhyloP100		0.40

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs734165;

hg19: chr10-111697789;