chr9-3129841-C-T

Variant names:

• chr9-3129841-C-T
• rs561867
• ENST00000497195.2:n.204+51707G>A

Variant summary

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

The ENST00000497195.2(ENSG00000290482):​n.204+51707G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.111 in 151,838 control chromosomes in the GnomAD database, including 1,066 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 0.11 (1066 hom., cov: 32)
• Consequence: ENSG00000290482 ENST00000497195.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.556
• Publications: 2 publications found

Genes affected

ENSG00000290482 (HGNC:):

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 (NFE) allele frequency at 95% confidence interval = 0.137 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000497195.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000290482	ENST00000497195.2	TSL:2	n.204+51707G>A		intron	N/A
	ENSG00000290482	ENST00000515723.2	TSL:5	n.208+51707G>A		intron	N/A
	ENSG00000290482	ENST00000716558.1		n.123+51707G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.111 AC: 16861 AN: 151720 Hom.: 1065 Cov.: 32

Gnomad AFR AF: 0.0635

Gnomad AMI AF: 0.144

Gnomad AMR AF: 0.101

Gnomad ASJ AF: 0.141

Gnomad EAS AF: 0.0930

Gnomad SAS AF: 0.128

Gnomad FIN AF: 0.119

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.139

Gnomad OTH AF: 0.106

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

GnomAD4 genome AF: 0.111 AC: 16861 AN: 151838 Hom.: 1066 Cov.: 32 AF XY: 0.109 AC XY: 8102 AN XY: 74192

African (AFR) AF: 0.0634 AC: 2627 AN: 41436

American (AMR) AF: 0.101 AC: 1535 AN: 15224

Ashkenazi Jewish (ASJ) AF: 0.141 AC: 490 AN: 3470

East Asian (EAS) AF: 0.0927 AC: 477 AN: 5148

South Asian (SAS) AF: 0.129 AC: 622 AN: 4820

European-Finnish (FIN) AF: 0.119 AC: 1255 AN: 10518

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.139 AC: 9465 AN: 67916

Other (OTH) AF: 0.108 AC: 226 AN: 2102

Alfa AF: 0.118 Hom.: 295

Bravo AF: 0.107

Asia WGS AF: 0.134 AC: 465 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	12
DANN	Benign	0.56
PhyloP100		0.56

Splicing

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

Other links and lift over

dbSNP: rs561867; hg19: chr9-3129841;