rs943430

Variant names:

• chr9-134474694-A-G
• rs943430
• XR_007061837.1:n.1969A>G

Variant summary

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

The XR_007061837.1(LOC105376311):​n.1969A>G 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 0.631 in 152,032 control chromosomes in the GnomAD database, including 31,611 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 0.63 (31611 hom., cov: 33)
• Consequence: LOC105376311 XR_007061837.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.72
• Publications: 2 publications found

Genes affected

LOC105376311 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.722 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105376311	XR_007061837.1	n.1969A>G		non_coding_transcript_exon_variant	Exon 2 of 6
LOC105376311	XR_007061838.1	n.1969A>G		non_coding_transcript_exon_variant	Exon 2 of 7
LOC105376311	XR_007061839.1	n.865A>G		non_coding_transcript_exon_variant	Exon 1 of 6
LOC105376311	XR_007061841.1	n.358-4189A>G		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000228877	ENST00000745249.1	n.212-4189A>G		intron_variant	Intron 2 of 7
ENSG00000228877	ENST00000745250.1	n.194+29374A>G		intron_variant	Intron 2 of 3
ENSG00000228877	ENST00000745251.1	n.120-4189A>G		intron_variant	Intron 1 of 5

Frequencies

GnomAD3 genomes AF: 0.631 AC: 95815 AN: 151914 Hom.: 31597 Cov.: 33

Gnomad AFR AF: 0.428

Gnomad AMI AF: 0.863

Gnomad AMR AF: 0.666

Gnomad ASJ AF: 0.735

Gnomad EAS AF: 0.586

Gnomad SAS AF: 0.534

Gnomad FIN AF: 0.752

Gnomad MID AF: 0.690

Gnomad NFE AF: 0.728

Gnomad OTH AF: 0.655

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

GnomAD4 genome AF: 0.631 AC: 95874 AN: 152032 Hom.: 31611 Cov.: 33 AF XY: 0.631 AC XY: 46878 AN XY: 74322

African (AFR) AF: 0.429 AC: 17777 AN: 41452

American (AMR) AF: 0.666 AC: 10180 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.735 AC: 2552 AN: 3470

East Asian (EAS) AF: 0.587 AC: 3016 AN: 5142

South Asian (SAS) AF: 0.534 AC: 2573 AN: 4822

European-Finnish (FIN) AF: 0.752 AC: 7960 AN: 10582

Middle Eastern (MID) AF: 0.670 AC: 197 AN: 294

European-Non Finnish (NFE) AF: 0.728 AC: 49460 AN: 67972

Other (OTH) AF: 0.652 AC: 1372 AN: 2104

Alfa AF: 0.687 Hom.: 108477

Bravo AF: 0.623

Asia WGS AF: 0.546 AC: 1896 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.79
DANN	Benign	0.62
PhyloP100		-3.7

Splicing

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

Other links and lift over

dbSNP: rs943430; hg19: chr9-137366540; COSMIC: COSV60405363;