rs9457880

Positions:

• chr6-160277707-C-A
• chr6-160277707-C-T

Variant summary

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

The XR_001744437.2(LOC105378088):​n.2082C>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 0.0432 in 152,192 control chromosomes in the GnomAD database, including 265 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 0.043 (265 hom., cov: 32)
  • Exomes 𝑓: 0.063 (0 hom.)
• Consequence: LOC105378088 XR_001744437.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.961

Genes affected

LOC105378088 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.173 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105378088	XR_001744437.2	n.2082C>A		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0433 AC: 6576 AN: 152042 Hom.: 265 Cov.: 32

Gnomad AFR AF: 0.0123

Gnomad AMI AF: 0.0164

Gnomad AMR AF: 0.0204

Gnomad ASJ AF: 0.0352

Gnomad EAS AF: 0.182

Gnomad SAS AF: 0.160

Gnomad FIN AF: 0.0772

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.0441

Gnomad OTH AF: 0.0445

GnomAD4 exome AF: 0.0625 AC: 2 AN: 32 Hom.: 0 AF XY: 0.0769 AC XY: 2 AN XY: 26

Gnomad4 AFR exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0769

GnomAD4 genome AF: 0.0432 AC: 6574 AN: 152160 Hom.: 265 Cov.: 32 AF XY: 0.0477 AC XY: 3547 AN XY: 74368

Gnomad4 AFR AF: 0.0123

Gnomad4 AMR AF: 0.0204

Gnomad4 ASJ AF: 0.0352

Gnomad4 EAS AF: 0.183

Gnomad4 SAS AF: 0.159

Gnomad4 FIN AF: 0.0772

Gnomad4 NFE AF: 0.0441

Gnomad4 OTH AF: 0.0440

Alfa AF: 0.0429 Hom.: 47

Bravo AF: 0.0355

Asia WGS AF: 0.188 AC: 652 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.094
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9457880; hg19: chr6-160698739;