chr9-100353890-G-A

Position:

• chr9-100353890-G-A

Variant summary

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

The XR_930174.2(LOC105376177):​n.621-107G>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 0.632 in 152,070 control chromosomes in the GnomAD database, including 32,275 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 0.63 (32275 hom., cov: 32)
• Consequence: LOC105376177 XR_930174.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.289

Genes affected

LOC105376177 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.872 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105376177	XR_930174.2	n.621-107G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.631 AC: 95935 AN: 151952 Hom.: 32225 Cov.: 32

Gnomad AFR AF: 0.829

Gnomad AMI AF: 0.283

Gnomad AMR AF: 0.677

Gnomad ASJ AF: 0.582

Gnomad EAS AF: 0.894

Gnomad SAS AF: 0.756

Gnomad FIN AF: 0.542

Gnomad MID AF: 0.617

Gnomad NFE AF: 0.494

Gnomad OTH AF: 0.610

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

GnomAD4 genome AF: 0.632 AC: 96051 AN: 152070 Hom.: 32275 Cov.: 32 AF XY: 0.638 AC XY: 47438 AN XY: 74328

Gnomad4 AFR AF: 0.829

Gnomad4 AMR AF: 0.677

Gnomad4 ASJ AF: 0.582

Gnomad4 EAS AF: 0.894

Gnomad4 SAS AF: 0.755

Gnomad4 FIN AF: 0.542

Gnomad4 NFE AF: 0.494

Gnomad4 OTH AF: 0.608

Alfa AF: 0.587 Hom.: 3976

Bravo AF: 0.648

Asia WGS AF: 0.792 AC: 2753 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.77
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1930243; hg19: chr9-103116172;