rs12352822

chr9-117785004-A-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000697639.1(ENSG00000284977):n.782+511A>G 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 0.103 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: ENST00000697639.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.409

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LOC105376244	XR_007061905.1	n.2648+511A>G		intron_variant, non_coding_transcript_variant
LOC105376244	XR_007061906.1	n.2065+511A>G		intron_variant, non_coding_transcript_variant
LOC105376244	XR_007061907.1	n.2146+17754A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000697639.1	n.782+511A>G		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.0411

Gnomad4 AMR AF: 0.117

Gnomad4 ASJ AF: 0.107

Gnomad4 EAS AF: 0.00735

Gnomad4 SAS AF: 0.123

Gnomad4 FIN AF: 0.137

Gnomad4 NFE AF: 0.139

Gnomad4 OTH AF: 0.107

Alfa AF: 0.129 Hom.: 2696

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12352822; hg19: chr9-120547282;