rs2375980

Positions:

• chr9-2692622-C-G

Variant summary

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

The XR_929436.3(LOC105375957):​n.1840G>C 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 0.509 in 152,058 control chromosomes in the GnomAD database, including 21,311 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 0.51 (21311 hom., cov: 33)
• Consequence: LOC105375957 XR_929436.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.572

Genes affected

LOC105375957 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.718 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105375957	XR_929436.3	n.1840G>C		non_coding_transcript_exon_variant	1/3

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.509 AC: 77303 AN: 151940 Hom.: 21271 Cov.: 33

Gnomad AFR AF: 0.724

Gnomad AMI AF: 0.347

Gnomad AMR AF: 0.493

Gnomad ASJ AF: 0.475

Gnomad EAS AF: 0.556

Gnomad SAS AF: 0.451

Gnomad FIN AF: 0.450

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.397

Gnomad OTH AF: 0.461

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

GnomAD4 genome AF: 0.509 AC: 77398 AN: 152058 Hom.: 21311 Cov.: 33 AF XY: 0.512 AC XY: 38063 AN XY: 74344

Gnomad4 AFR AF: 0.725

Gnomad4 AMR AF: 0.493

Gnomad4 ASJ AF: 0.475

Gnomad4 EAS AF: 0.557

Gnomad4 SAS AF: 0.450

Gnomad4 FIN AF: 0.450

Gnomad4 NFE AF: 0.397

Gnomad4 OTH AF: 0.458

Alfa AF: 0.454 Hom.: 2098

Bravo AF: 0.520

Asia WGS AF: 0.528 AC: 1835 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.88
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: rs2375980; hg19: chr9-2692622;