rs1455177

Variant names:

• chr9-3792613-C-G
• rs1455177
• XR_929442.3:n.481+256C>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+256C>G variant causes a intron 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.15
• Publications: 2 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=-0.91).
• 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 rank	MANE	Protein	UniProt
LOC105375962	XR_929442.3	n.481+256C>G		intron_variant	Intron 2 of 3

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.447 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

African (AFR) AF: 0.275 AC: 11363 AN: 41378

American (AMR) AF: 0.436 AC: 6652 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.568 AC: 1973 AN: 3472

East Asian (EAS) AF: 0.524 AC: 2716 AN: 5180

South Asian (SAS) AF: 0.442 AC: 2127 AN: 4808

European-Finnish (FIN) AF: 0.391 AC: 4118 AN: 10528

Middle Eastern (MID) AF: 0.473 AC: 139 AN: 294

European-Non Finnish (NFE) AF: 0.547 AC: 37159 AN: 67934

Other (OTH) AF: 0.491 AC: 1036 AN: 2108

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
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs1455177; hg19: chr9-3792613;