9-71914717-T-G

Variant names:

• chr9-71914717-T-G
• rs1359254
• NM_182505.5:c.102+2881T>G

Variant summary

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

The NM_182505.5(C9orf85):​c.102+2881T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.935 in 152,260 control chromosomes in the GnomAD database, including 67,272 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 (67272 hom., cov: 31)
• Consequence: C9orf85 NM_182505.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00400
• Publications: 2 publications found

Genes affected

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.58).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.989 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_182505.5. 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
	C9orf85	NM_182505.5	MANE Select	c.102+2881T>G		intron	N/A	NP_872311.2
	C9orf85	NM_001365053.2		c.102+2881T>G		intron	N/A	NP_001351982.1	Q96MD7-3
	C9orf85	NM_001365055.2		c.-87+2881T>G		intron	N/A	NP_001351984.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C9orf85	ENST00000334731.7	TSL:1 MANE Select	c.102+2881T>G		intron	N/A	ENSP00000334289.2	Q96MD7-1
	C9orf85	ENST00000479413.1	TSL:1	n.102+2881T>G		intron	N/A	ENSP00000433086.1	Q96MD7-2
	C9orf85	ENST00000377031.7	TSL:3	c.102+2881T>G		intron	N/A	ENSP00000366230.3	Q96MD7-3

Frequencies

GnomAD3 genomes AF: 0.936 AC: 142390 AN: 152144 Hom.: 67277 Cov.: 31

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: 0.935 AC: 142424 AN: 152260 Hom.: 67272 Cov.: 31 AF XY: 0.937 AC XY: 69773 AN XY: 74438

African (AFR) AF: 0.790 AC: 32782 AN: 41518

American (AMR) AF: 0.972 AC: 14868 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.976 AC: 3389 AN: 3472

East Asian (EAS) AF: 1.00 AC: 5165 AN: 5166

South Asian (SAS) AF: 0.990 AC: 4779 AN: 4828

European-Finnish (FIN) AF: 0.994 AC: 10555 AN: 10618

Middle Eastern (MID) AF: 0.956 AC: 281 AN: 294

European-Non Finnish (NFE) AF: 0.995 AC: 67698 AN: 68040

Other (OTH) AF: 0.945 AC: 1995 AN: 2110

Alfa AF: 0.966 Hom.: 21122

Bravo AF: 0.926

Asia WGS AF: 0.958 AC: 3330 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.58
CADD	Benign	11
DANN	Benign	0.92
PhyloP100		0.0040
Mutation Taster		=100/0	polymorphism (auto)

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1359254;

hg19: chr9-74529633;