rs1110183

Positions:

• chr9-38456368-G-A

Variant summary

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

The ENST00000635962.1(ENSG00000291061):​n.647+175G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.229 in 152,110 control chromosomes in the GnomAD database, including 4,524 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 0.23 (4524 hom., cov: 32)
• Consequence: ENSG00000291061 ENST00000635962.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.14

Genes affected

ENSG00000291061 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.543 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105376041	XR_007061484.1	n.1208+175G>A		intron_variant
LOC105376041	XR_007061485.1	n.847+175G>A		intron_variant
LOC105376041	XR_007061486.1	n.847+175G>A		intron_variant
LOC105376041	XR_007061487.1	n.847+175G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000291061	ENST00000635962.1	n.647+175G>A		intron_variant		5
ENSG00000283162	ENST00000636076.1	n.76+175G>A		intron_variant		6
ENSG00000291061	ENST00000637760.3	n.649+175G>A		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.229 AC: 34855 AN: 151992 Hom.: 4517 Cov.: 32

Gnomad AFR AF: 0.136

Gnomad AMI AF: 0.318

Gnomad AMR AF: 0.268

Gnomad ASJ AF: 0.239

Gnomad EAS AF: 0.561

Gnomad SAS AF: 0.276

Gnomad FIN AF: 0.205

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.250

Gnomad OTH AF: 0.258

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

GnomAD4 genome AF: 0.229 AC: 34879 AN: 152110 Hom.: 4524 Cov.: 32 AF XY: 0.231 AC XY: 17172 AN XY: 74356

Gnomad4 AFR AF: 0.136

Gnomad4 AMR AF: 0.268

Gnomad4 ASJ AF: 0.239

Gnomad4 EAS AF: 0.560

Gnomad4 SAS AF: 0.276

Gnomad4 FIN AF: 0.205

Gnomad4 NFE AF: 0.250

Gnomad4 OTH AF: 0.264

Alfa AF: 0.253 Hom.: 11040

Bravo AF: 0.230

Asia WGS AF: 0.376 AC: 1309 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.11
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1110183; hg19: chr9-38456365;