chr9-23664509-C-T

Variant names:

• chr9-23664509-C-T
• rs2116226
• ENST00000640307.1:n.433-1492G>A

Variant summary

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

The ENST00000640307.1(ENSG00000283982):​n.433-1492G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.70 (31695 hom., cov: 20)
• Consequence: ENSG00000283982 ENST00000640307.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.121
• Publications: 1 publications found

Genes affected

ENSG00000283982 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.752 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000640307.1. 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
	LOC101929563	NR_121602.1		n.445-1492G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000283982	ENST00000640307.1	TSL:1	n.433-1492G>A		intron	N/A
	ENSG00000283982	ENST00000804428.1		n.352+7220G>A		intron	N/A
	ENSG00000283982	ENST00000804429.1		n.197+7780G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.695 AC: 93977 AN: 135232 Hom.: 31678 Cov.: 20

Gnomad AFR AF: 0.563

Gnomad AMI AF: 0.703

Gnomad AMR AF: 0.764

Gnomad ASJ AF: 0.719

Gnomad EAS AF: 0.660

Gnomad SAS AF: 0.750

Gnomad FIN AF: 0.758

Gnomad MID AF: 0.739

Gnomad NFE AF: 0.738

Gnomad OTH AF: 0.686

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

GnomAD4 genome AF: 0.695 AC: 94010 AN: 135264 Hom.: 31695 Cov.: 20 AF XY: 0.699 AC XY: 45429 AN XY: 64994

African (AFR) AF: 0.563 AC: 18830 AN: 33448

American (AMR) AF: 0.765 AC: 10447 AN: 13664

Ashkenazi Jewish (ASJ) AF: 0.719 AC: 2439 AN: 3390

East Asian (EAS) AF: 0.660 AC: 3032 AN: 4592

South Asian (SAS) AF: 0.750 AC: 3228 AN: 4302

European-Finnish (FIN) AF: 0.758 AC: 5881 AN: 7762

Middle Eastern (MID) AF: 0.742 AC: 184 AN: 248

European-Non Finnish (NFE) AF: 0.738 AC: 48074 AN: 65120

Other (OTH) AF: 0.687 AC: 1289 AN: 1876

Alfa AF: 0.644 Hom.: 2537

Bravo AF: 0.651

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.9
DANN	Benign	0.42
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs2116226; hg19: chr9-23664507;