9-87416754-G-C

Variant names:

• chr9-87416754-G-C
• rs1806864

Variant summary

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

The variant allele was found at a frequency of 0.0726 in 152,002 control chromosomes in the GnomAD database, including 511 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 0.073 (511 hom., cov: 31)
• Consequence: LOC112268032 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.78
• Publications: 6 publications found

Genes affected

LOC112268032 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0936 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000804137.1. 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
	ENSG00000289166	ENST00000804137.1		n.32+6299C>G		intron	N/A
	ENSG00000289166	ENST00000804138.1		n.32+6299C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0726 AC: 11026 AN: 151884 Hom.: 509 Cov.: 31

Gnomad AFR AF: 0.0490

Gnomad AMI AF: 0.0603

Gnomad AMR AF: 0.0697

Gnomad ASJ AF: 0.0987

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.0162

Gnomad FIN AF: 0.0764

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0955

Gnomad OTH AF: 0.0662

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

GnomAD4 genome AF: 0.0726 AC: 11037 AN: 152002 Hom.: 511 Cov.: 31 AF XY: 0.0691 AC XY: 5137 AN XY: 74306

African (AFR) AF: 0.0492 AC: 2036 AN: 41394

American (AMR) AF: 0.0697 AC: 1065 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.0987 AC: 342 AN: 3466

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5176

South Asian (SAS) AF: 0.0162 AC: 78 AN: 4814

European-Finnish (FIN) AF: 0.0764 AC: 808 AN: 10572

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.0955 AC: 6495 AN: 67996

Other (OTH) AF: 0.0655 AC: 138 AN: 2106

Alfa AF: 0.0876 Hom.: 394

Bravo AF: 0.0712

Asia WGS AF: 0.0120 AC: 43 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.7
DANN	Benign	0.47
PhyloP100		1.8

Splicing

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

Other links and lift over

dbSNP: rs1806864; hg19: chr9-90031669;