9-95606595-C-A

Variant names:

• chr9-95606595-C-A
• rs3824491
• ENST00000748151.1:n.218C>A

Variant summary

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

The ENST00000748151.1(ENSG00000297470):​n.218C>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0858 in 152,186 control chromosomes in the GnomAD database, including 616 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 0.086 (616 hom., cov: 32)
• Consequence: ENSG00000297470 ENST00000748151.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.25
• Publications: 2 publications found

Genes affected

ENSG00000297470 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.102 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000748151.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000297470	ENST00000748151.1		n.218C>A		non_coding_transcript_exon	Exon 1 of 2

Frequencies

GnomAD3 genomes AF: 0.0858 AC: 13049 AN: 152068 Hom.: 615 Cov.: 32

Gnomad AFR AF: 0.0872

Gnomad AMI AF: 0.231

Gnomad AMR AF: 0.0575

Gnomad ASJ AF: 0.116

Gnomad EAS AF: 0.0697

Gnomad SAS AF: 0.110

Gnomad FIN AF: 0.0974

Gnomad MID AF: 0.0860

Gnomad NFE AF: 0.0858

Gnomad OTH AF: 0.0789

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

GnomAD4 genome AF: 0.0858 AC: 13058 AN: 152186 Hom.: 616 Cov.: 32 AF XY: 0.0870 AC XY: 6470 AN XY: 74410

African (AFR) AF: 0.0872 AC: 3620 AN: 41500

American (AMR) AF: 0.0575 AC: 879 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.116 AC: 402 AN: 3470

East Asian (EAS) AF: 0.0699 AC: 362 AN: 5180

South Asian (SAS) AF: 0.110 AC: 531 AN: 4828

European-Finnish (FIN) AF: 0.0974 AC: 1031 AN: 10584

Middle Eastern (MID) AF: 0.0856 AC: 25 AN: 292

European-Non Finnish (NFE) AF: 0.0858 AC: 5833 AN: 68010

Other (OTH) AF: 0.0777 AC: 164 AN: 2112

Alfa AF: 0.0764 Hom.: 276

Bravo AF: 0.0822

Asia WGS AF: 0.0720 AC: 252 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.032
DANN	Benign	0.72
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs3824491; hg19: chr9-98368877;