9-102254467-G-A

Position:

• chr9-102254467-G-A

Variant summary

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

The XR_930189.2(LOC105376188):​n.190-4718G>A 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 0.163 in 152,048 control chromosomes in the GnomAD database, including 3,348 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 0.16 (3348 hom., cov: 32)
• Consequence: LOC105376188 XR_930189.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.512

Genes affected

LOC105376188 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.694 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105376188	XR_930189.2	n.190-4718G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.163 AC: 24794 AN: 151930 Hom.: 3351 Cov.: 32

Gnomad AFR AF: 0.245

Gnomad AMI AF: 0.179

Gnomad AMR AF: 0.152

Gnomad ASJ AF: 0.0634

Gnomad EAS AF: 0.713

Gnomad SAS AF: 0.352

Gnomad FIN AF: 0.0443

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0852

Gnomad OTH AF: 0.157

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

GnomAD4 genome AF: 0.163 AC: 24822 AN: 152048 Hom.: 3348 Cov.: 32 AF XY: 0.170 AC XY: 12608 AN XY: 74332

Gnomad4 AFR AF: 0.245

Gnomad4 AMR AF: 0.153

Gnomad4 ASJ AF: 0.0634

Gnomad4 EAS AF: 0.713

Gnomad4 SAS AF: 0.351

Gnomad4 FIN AF: 0.0443

Gnomad4 NFE AF: 0.0852

Gnomad4 OTH AF: 0.160

Alfa AF: 0.118 Hom.: 794

Bravo AF: 0.175

Asia WGS AF: 0.474 AC: 1646 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.6
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1535628; hg19: chr9-105016749;