rs6475920

Positions:

• chr9-2673933-C-A
• chr9-2673933-C-G

Variant summary

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

The XR_929436.3(LOC105375957):​n.20529G>T 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 0.486 in 151,968 control chromosomes in the GnomAD database, including 20,311 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 0.49 (20311 hom., cov: 32)
• Consequence: LOC105375957 XR_929436.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0920

Genes affected

LOC105375957 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.755 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105375957	XR_929436.3	n.20529G>T		non_coding_transcript_exon_variant	1/3
		n.2673933C>A		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.486 AC: 73746 AN: 151848 Hom.: 20268 Cov.: 32

Gnomad AFR AF: 0.762

Gnomad AMI AF: 0.319

Gnomad AMR AF: 0.433

Gnomad ASJ AF: 0.502

Gnomad EAS AF: 0.418

Gnomad SAS AF: 0.413

Gnomad FIN AF: 0.343

Gnomad MID AF: 0.456

Gnomad NFE AF: 0.365

Gnomad OTH AF: 0.443

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

GnomAD4 genome AF: 0.486 AC: 73852 AN: 151968 Hom.: 20311 Cov.: 32 AF XY: 0.484 AC XY: 35912 AN XY: 74272

Gnomad4 AFR AF: 0.762

Gnomad4 AMR AF: 0.433

Gnomad4 ASJ AF: 0.502

Gnomad4 EAS AF: 0.419

Gnomad4 SAS AF: 0.414

Gnomad4 FIN AF: 0.343

Gnomad4 NFE AF: 0.365

Gnomad4 OTH AF: 0.441

Alfa AF: 0.400 Hom.: 4093

Bravo AF: 0.502

Asia WGS AF: 0.443 AC: 1541 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.1
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6475920; hg19: chr9-2673933; COSMIC: COSV60321896;