9-1926444-T-C

Variant names:

• chr9-1926444-T-C
• rs7045276
• XR_929422.3:n.1349A>G

Variant summary

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

The XR_929422.3(LOC105375952):​n.1349A>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 0.407 in 152,090 control chromosomes in the GnomAD database, including 17,290 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 0.41 (17290 hom., cov: 32)
• Consequence: LOC105375952 XR_929422.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.215
• Publications: 4 publications found

Genes affected

LOC105375952 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.778 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105375952	XR_929422.3	n.1349A>G		non_coding_transcript_exon_variant	Exon 3 of 3
LOC105375951	XR_001746599.1	n.143-35677T>C		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000295589	ENST00000731080.1	n.470+812T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.407 AC: 61794 AN: 151972 Hom.: 17229 Cov.: 32

Gnomad AFR AF: 0.785

Gnomad AMI AF: 0.0998

Gnomad AMR AF: 0.373

Gnomad ASJ AF: 0.208

Gnomad EAS AF: 0.529

Gnomad SAS AF: 0.400

Gnomad FIN AF: 0.260

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.215

Gnomad OTH AF: 0.336

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

GnomAD4 genome AF: 0.407 AC: 61916 AN: 152090 Hom.: 17290 Cov.: 32 AF XY: 0.410 AC XY: 30461 AN XY: 74336

African (AFR) AF: 0.785 AC: 32544 AN: 41450

American (AMR) AF: 0.373 AC: 5710 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.208 AC: 722 AN: 3470

East Asian (EAS) AF: 0.530 AC: 2738 AN: 5168

South Asian (SAS) AF: 0.398 AC: 1918 AN: 4814

European-Finnish (FIN) AF: 0.260 AC: 2748 AN: 10588

Middle Eastern (MID) AF: 0.282 AC: 83 AN: 294

European-Non Finnish (NFE) AF: 0.215 AC: 14646 AN: 67996

Other (OTH) AF: 0.339 AC: 716 AN: 2110

Alfa AF: 0.290 Hom.: 15715

Bravo AF: 0.433

Asia WGS AF: 0.480 AC: 1670 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.8
DANN	Benign	0.39
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs7045276; hg19: chr9-1926444;