rs9275659

Positions:

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

Variant summary

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

The XR_001743875.3(LOC102725019):​n.308C>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: LOC102725019 XR_001743875.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.41

Genes affected

LOC102725019 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC102725019	XR_001743875.3	n.308C>A		non_coding_transcript_exon_variant	1/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000448198.2	n.143+179C>A		intron_variant, non_coding_transcript_variant		2
	ENST00000585372.2	n.298C>A		non_coding_transcript_exon_variant	1/2	3
	ENST00000621553.1	n.120-80C>A		intron_variant, non_coding_transcript_variant		5

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

Gnomad4 FIN exome AF: 0.00

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

Gnomad4 AFR AF: 0.306

Gnomad4 AMR AF: 0.186

Gnomad4 ASJ AF: 0.246

Gnomad4 EAS AF: 0.138

Gnomad4 SAS AF: 0.120

Gnomad4 FIN AF: 0.188

Gnomad4 NFE AF: 0.207

Gnomad4 OTH AF: 0.231

Alfa AF: 0.196 Hom.: 3195

Bravo AF: 0.227

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9275659; hg19: chr6-32686103;