9-3796061-C-G

Variant names:

• chr9-3796061-C-G
• rs1455175
• XR_929442.3:n.481+3704C>G

Variant summary

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

The XR_929442.3(LOC105375962):​n.481+3704C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.717 in 151,898 control chromosomes in the GnomAD database, including 40,381 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 0.72 (40381 hom., cov: 31)
• Consequence: LOC105375962 XR_929442.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0250
• Publications: 3 publications found

Genes affected

LOC105375962 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.839 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105375962	XR_929442.3	n.481+3704C>G		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.718 AC: 108904 AN: 151780 Hom.: 40362 Cov.: 31

Gnomad AFR AF: 0.515

Gnomad AMI AF: 0.638

Gnomad AMR AF: 0.779

Gnomad ASJ AF: 0.841

Gnomad EAS AF: 0.861

Gnomad SAS AF: 0.840

Gnomad FIN AF: 0.817

Gnomad MID AF: 0.832

Gnomad NFE AF: 0.785

Gnomad OTH AF: 0.747

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

GnomAD4 genome AF: 0.717 AC: 108964 AN: 151898 Hom.: 40381 Cov.: 31 AF XY: 0.723 AC XY: 53684 AN XY: 74212

African (AFR) AF: 0.515 AC: 21331 AN: 41392

American (AMR) AF: 0.779 AC: 11894 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.841 AC: 2917 AN: 3468

East Asian (EAS) AF: 0.860 AC: 4450 AN: 5172

South Asian (SAS) AF: 0.840 AC: 4040 AN: 4812

European-Finnish (FIN) AF: 0.817 AC: 8609 AN: 10532

Middle Eastern (MID) AF: 0.820 AC: 241 AN: 294

European-Non Finnish (NFE) AF: 0.785 AC: 53317 AN: 67942

Other (OTH) AF: 0.750 AC: 1584 AN: 2112

Alfa AF: 0.677 Hom.: 2400

Bravo AF: 0.705

Asia WGS AF: 0.833 AC: 2897 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	8.2
DANN	Benign	0.72
PhyloP100		0.025

Splicing

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

Other links and lift over

dbSNP: rs1455175; hg19: chr9-3796061;