rs6475920

Variant names:

• chr9-2673933-C-A
• rs6475920
• XR_929436.3:n.20529G>T

Your query was ambiguous. Multiple possible variants found:

• chr9-2673933-C-A
• chr9-2673933-C-G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

Genes affected

LOC105375957 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000768783.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000286670	ENST00000768783.1		n.114-5872G>T		intron	N/A
	ENSG00000286670	ENST00000768784.1		n.157-5872G>T		intron	N/A
	ENSG00000286670	ENST00000768785.1		n.157-8858G>T		intron	N/A

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

African (AFR) AF: 0.762 AC: 31584 AN: 41452

American (AMR) AF: 0.433 AC: 6614 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.502 AC: 1742 AN: 3472

East Asian (EAS) AF: 0.419 AC: 2158 AN: 5156

South Asian (SAS) AF: 0.414 AC: 1989 AN: 4810

European-Finnish (FIN) AF: 0.343 AC: 3618 AN: 10538

Middle Eastern (MID) AF: 0.466 AC: 137 AN: 294

European-Non Finnish (NFE) AF: 0.365 AC: 24791 AN: 67962

Other (OTH) AF: 0.441 AC: 929 AN: 2106

Alfa AF: 0.405 Hom.: 5219

Bravo AF: 0.502

Asia WGS AF: 0.443 AC: 1541 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.1
DANN	Benign	0.74
PhyloP100		-0.092

Splicing

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

Other links and lift over

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