rs12352822

Variant names:

• chr9-117785004-A-G
• rs12352822
• ENST00000697666.1:c.141-63061A>G

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000697666.1(ENSG00000285082):​c.141-63061A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.103 in 152,162 control chromosomes in the GnomAD database, including 984 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 0.10 (984 hom., cov: 32)
• Consequence: ENSG00000285082 ENST00000697666.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.409
• Publications: 4 publications found

Genes affected

ENSG00000285082 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.25).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.136 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105376244	XR_007061905.1	n.2648+511A>G		intron_variant	Intron 5 of 7
LOC105376244	XR_007061906.1	n.2065+511A>G		intron_variant	Intron 6 of 8
LOC105376244	XR_007061907.1	n.2146+17754A>G		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000285082	ENST00000697666.1	c.141-63061A>G		intron_variant	Intron 3 of 4			ENSP00000513391.1

Frequencies

GnomAD3 genomes AF: 0.104 AC: 15748 AN: 152044 Hom.: 985 Cov.: 32

Gnomad AFR AF: 0.0412

Gnomad AMI AF: 0.104

Gnomad AMR AF: 0.117

Gnomad ASJ AF: 0.107

Gnomad EAS AF: 0.00733

Gnomad SAS AF: 0.123

Gnomad FIN AF: 0.137

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.139

Gnomad OTH AF: 0.108

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

GnomAD4 genome AF: 0.103 AC: 15743 AN: 152162 Hom.: 984 Cov.: 32 AF XY: 0.103 AC XY: 7632 AN XY: 74390

African (AFR) AF: 0.0411 AC: 1707 AN: 41524

American (AMR) AF: 0.117 AC: 1783 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.107 AC: 373 AN: 3472

East Asian (EAS) AF: 0.00735 AC: 38 AN: 5170

South Asian (SAS) AF: 0.123 AC: 594 AN: 4824

European-Finnish (FIN) AF: 0.137 AC: 1457 AN: 10600

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.139 AC: 9429 AN: 67976

Other (OTH) AF: 0.107 AC: 226 AN: 2116

Alfa AF: 0.125 Hom.: 5569

Bravo AF: 0.0960

Asia WGS AF: 0.0570 AC: 201 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.25
CADD	Benign	16
DANN	Benign	0.80
PhyloP100		0.41

Splicing

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

Other links and lift over

dbSNP: rs12352822; hg19: chr9-120547282;