rs9275659

Variant names:

• chr6-32718326-C-A
• rs9275659
• ENST00000585372.2:n.298C>A

Your query was ambiguous. Multiple possible variants found:

• chr6-32718326-C-A
• chr6-32718326-C-G
• chr6-32718326-C-T

Variant summary

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

The ENST00000585372.2(ENSG00000232080):​n.298C>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 0.226 in 151,940 control chromosomes in the GnomAD database, including 4,095 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 0.23 (4095 hom., cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000232080 ENST00000585372.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.41
• Publications: 24 publications found

Genes affected

ENSG00000232080 (HGNC:39763):

LOC102725019 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.302 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000585372.2. 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
	LOC102725019	NR_190902.1		n.129+179C>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000232080	ENST00000585372.2	TSL:3	n.298C>A		non_coding_transcript_exon	Exon 1 of 2
	ENSG00000232080	ENST00000448198.3	TSL:2	n.145+179C>A		intron	N/A
	ENSG00000232080	ENST00000621553.1	TSL:5	n.120-80C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.226 AC: 34314 AN: 151822 Hom.: 4085 Cov.: 32

Gnomad AFR AF: 0.306

Gnomad AMI AF: 0.0824

Gnomad AMR AF: 0.186

Gnomad ASJ AF: 0.246

Gnomad EAS AF: 0.138

Gnomad SAS AF: 0.120

Gnomad FIN AF: 0.188

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.207

Gnomad OTH AF: 0.234

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 2 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.226 AC: 34347 AN: 151940 Hom.: 4095 Cov.: 32 AF XY: 0.221 AC XY: 16393 AN XY: 74276

African (AFR) AF: 0.306 AC: 12673 AN: 41408

American (AMR) AF: 0.186 AC: 2840 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.246 AC: 854 AN: 3468

East Asian (EAS) AF: 0.138 AC: 710 AN: 5156

South Asian (SAS) AF: 0.120 AC: 576 AN: 4808

European-Finnish (FIN) AF: 0.188 AC: 1988 AN: 10550

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.207 AC: 14078 AN: 67968

Other (OTH) AF: 0.231 AC: 487 AN: 2108

Alfa AF: 0.212 Hom.: 11795

Bravo AF: 0.227

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	4.3
DANN	Benign	0.38
PhyloP100		-1.4

Splicing

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: rs9275659;

hg19: chr6-32686103;