rs2310333

Positions:

• chr9-73092464-A-G

Variant summary

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

The XR_929928.2(LOC105376081):​n.216-467T>C 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 0.606 in 151,866 control chromosomes in the GnomAD database, including 28,994 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 0.61 (28994 hom., cov: 31)
• Consequence: LOC105376081 XR_929928.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.323

Genes affected

LOC105376081 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.679 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105376081	XR_929928.2	n.216-467T>C		intron_variant, non_coding_transcript_variant
LOC105376081	XR_929926.2	n.407-467T>C		intron_variant, non_coding_transcript_variant
LOC105376081	XR_929927.2	n.344-467T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.606 AC: 91922 AN: 151746 Hom.: 28972 Cov.: 31

Gnomad AFR AF: 0.427

Gnomad AMI AF: 0.732

Gnomad AMR AF: 0.655

Gnomad ASJ AF: 0.617

Gnomad EAS AF: 0.458

Gnomad SAS AF: 0.673

Gnomad FIN AF: 0.747

Gnomad MID AF: 0.627

Gnomad NFE AF: 0.685

Gnomad OTH AF: 0.642

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

GnomAD4 genome AF: 0.606 AC: 91994 AN: 151866 Hom.: 28994 Cov.: 31 AF XY: 0.610 AC XY: 45294 AN XY: 74216

Gnomad4 AFR AF: 0.427

Gnomad4 AMR AF: 0.655

Gnomad4 ASJ AF: 0.617

Gnomad4 EAS AF: 0.458

Gnomad4 SAS AF: 0.674

Gnomad4 FIN AF: 0.747

Gnomad4 NFE AF: 0.685

Gnomad4 OTH AF: 0.639

Alfa AF: 0.662 Hom.: 15273

Bravo AF: 0.588

Asia WGS AF: 0.565 AC: 1969 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.80
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2310333; hg19: chr9-75707380;