chr9-3792613-C-G

Position:

• chr9-3792613-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+256C>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 0.447 in 151,876 control chromosomes in the GnomAD database, including 16,356 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 0.45 (16356 hom., cov: 31)
• Consequence: LOC105375962 XR_929442.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.15

Genes affected

LOC105375962 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.542 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105375962	XR_929442.3	n.481+256C>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.447 AC: 67833 AN: 151756 Hom.: 16355 Cov.: 31

Gnomad AFR AF: 0.275

Gnomad AMI AF: 0.615

Gnomad AMR AF: 0.437

Gnomad ASJ AF: 0.568

Gnomad EAS AF: 0.525

Gnomad SAS AF: 0.443

Gnomad FIN AF: 0.391

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.547

Gnomad OTH AF: 0.491

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

GnomAD4 genome AF: 0.447 AC: 67844 AN: 151876 Hom.: 16356 Cov.: 31 AF XY: 0.439 AC XY: 32607 AN XY: 74220

Gnomad4 AFR AF: 0.275

Gnomad4 AMR AF: 0.436

Gnomad4 ASJ AF: 0.568

Gnomad4 EAS AF: 0.524

Gnomad4 SAS AF: 0.442

Gnomad4 FIN AF: 0.391

Gnomad4 NFE AF: 0.547

Gnomad4 OTH AF: 0.491

Alfa AF: 0.488 Hom.: 2319

Bravo AF: 0.442

Asia WGS AF: 0.443 AC: 1541 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.082
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1455177; hg19: chr9-3792613;