9-3796061-C-G

Position:

• chr9-3796061-C-G

Variant summary

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

The XR_929442.3(LOC105375962):​n.481+3704C>G variant causes a intron, non coding transcript 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0250

Genes affected

LOC105375962 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LOC105375962	XR_929442.3	n.481+3704C>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.515

Gnomad4 AMR AF: 0.779

Gnomad4 ASJ AF: 0.841

Gnomad4 EAS AF: 0.860

Gnomad4 SAS AF: 0.840

Gnomad4 FIN AF: 0.817

Gnomad4 NFE AF: 0.785

Gnomad4 OTH AF: 0.750

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1455175; hg19: chr9-3796061;