rs7030498

Positions:

• chr9-71984735-A-G

Variant summary

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

The NM_001365053.2(C9orf85):​c.*1862A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.609 in 152,220 control chromosomes in the GnomAD database, including 28,447 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 0.61 (28434 hom., cov: 34)
  • Exomes 𝑓: 0.68 (13 hom.)
• Consequence: C9orf85 NM_001365053.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.690

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=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.706 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
C9orf85	NM_001365053.2	c.*1862A>G		3_prime_UTR_variant	4/4
C9orf85	NM_001365057.2	c.*2078A>G		3_prime_UTR_variant	3/3
C9orf85	NR_157408.2	n.2515A>G		non_coding_transcript_exon_variant	4/4
C9orf85	NR_157409.2	n.2602A>G		non_coding_transcript_exon_variant	5/5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
C9orf85	ENST00000486911.2	c.*1718A>G		3_prime_UTR_variant	3/3	5

Frequencies

GnomAD3 genomes AF: 0.610 AC: 92679 AN: 152052 Hom.: 28424 Cov.: 34

Gnomad AFR AF: 0.573

Gnomad AMI AF: 0.568

Gnomad AMR AF: 0.664

Gnomad ASJ AF: 0.565

Gnomad EAS AF: 0.726

Gnomad SAS AF: 0.675

Gnomad FIN AF: 0.584

Gnomad MID AF: 0.570

Gnomad NFE AF: 0.613

Gnomad OTH AF: 0.615

GnomAD4 exome AF: 0.680 AC: 34 AN: 50 Hom.: 13 Cov.: 0 AF XY: 0.725 AC XY: 29 AN XY: 40

Gnomad4 AMR exome AF: 0.500

Gnomad4 EAS exome AF: 1.00

Gnomad4 SAS exome AF: 1.00

Gnomad4 NFE exome AF: 0.643

GnomAD4 genome AF: 0.609 AC: 92722 AN: 152170 Hom.: 28434 Cov.: 34 AF XY: 0.611 AC XY: 45457 AN XY: 74398

Gnomad4 AFR AF: 0.572

Gnomad4 AMR AF: 0.664

Gnomad4 ASJ AF: 0.565

Gnomad4 EAS AF: 0.725

Gnomad4 SAS AF: 0.675

Gnomad4 FIN AF: 0.584

Gnomad4 NFE AF: 0.613

Gnomad4 OTH AF: 0.617

Alfa AF: 0.609 Hom.: 57414

Bravo AF: 0.608

Asia WGS AF: 0.695 AC: 2418 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	5.4
DANN	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7030498; hg19: chr9-74599651;