rs4745138

chr9-71950971-G-Achr9-71950971-G-Cchr9-71950971-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_182505.5(C9orf85):c.209+3859G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.936 in 152,236 control chromosomes in the GnomAD database, including 67,279 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 0.94 (67279 hom., cov: 32)
• Consequence: C9orf85 NM_182505.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.01

Genes affected

C9orf85 (HGNC:28784): (chromosome 9 open reading frame 85)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.989 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
C9orf85	NM_182505.5	c.209+3859G>A		intron_variant		ENST00000334731.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
C9orf85	ENST00000334731.7	c.209+3859G>A		intron_variant		1	NM_182505.5	P1

Frequencies

GnomAD3 genomes AF: 0.936 AC: 142380 AN: 152116 Hom.: 67282 Cov.: 32

Gnomad AFR AF: 0.791

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.972

Gnomad ASJ AF: 0.976

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.990

Gnomad FIN AF: 0.994

Gnomad MID AF: 0.959

Gnomad NFE AF: 0.995

Gnomad OTH AF: 0.949

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

GnomAD4 genome AF: 0.936 AC: 142417 AN: 152236 Hom.: 67279 Cov.: 32 AF XY: 0.938 AC XY: 69797 AN XY: 74450

Gnomad4 AFR AF: 0.790

Gnomad4 AMR AF: 0.972

Gnomad4 ASJ AF: 0.976

Gnomad4 EAS AF: 1.00

Gnomad4 SAS AF: 0.990

Gnomad4 FIN AF: 0.994

Gnomad4 NFE AF: 0.995

Gnomad4 OTH AF: 0.945

Alfa AF: 0.965 Hom.: 4685

Bravo AF: 0.927

Asia WGS AF: 0.958 AC: 3328 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	0.0090
Dann	Benign	0.84

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs4745138; hg19: chr9-74565887;