rs1342022

Positions:

• chr9-73090591-G-A
• chr9-73090591-G-T

Variant summary

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

The XR_929928.2(LOC105376081):​n.1622C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.573 in 151,862 control chromosomes in the GnomAD database, including 26,992 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 0.57 (26992 hom., cov: 32)
• Consequence: LOC105376081 XR_929928.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.295

Genes affected

LOC105376081 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.678 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105376081	XR_929928.2	n.1622C>T		non_coding_transcript_exon_variant	3/3
LOC105376081	XR_929926.2	n.1813C>T		non_coding_transcript_exon_variant	4/4
LOC105376081	XR_929927.2	n.1750C>T		non_coding_transcript_exon_variant	4/4

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.573 AC: 86906 AN: 151744 Hom.: 26980 Cov.: 32

Gnomad AFR AF: 0.316

Gnomad AMI AF: 0.736

Gnomad AMR AF: 0.638

Gnomad ASJ AF: 0.618

Gnomad EAS AF: 0.455

Gnomad SAS AF: 0.657

Gnomad FIN AF: 0.748

Gnomad MID AF: 0.601

Gnomad NFE AF: 0.684

Gnomad OTH AF: 0.616

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

GnomAD4 genome AF: 0.573 AC: 86965 AN: 151862 Hom.: 26992 Cov.: 32 AF XY: 0.578 AC XY: 42903 AN XY: 74208

Gnomad4 AFR AF: 0.317

Gnomad4 AMR AF: 0.638

Gnomad4 ASJ AF: 0.618

Gnomad4 EAS AF: 0.455

Gnomad4 SAS AF: 0.658

Gnomad4 FIN AF: 0.748

Gnomad4 NFE AF: 0.684

Gnomad4 OTH AF: 0.614

Alfa AF: 0.638 Hom.: 14329

Bravo AF: 0.550

Asia WGS AF: 0.547 AC: 1900 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.7
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1342022; hg19: chr9-75705507;