rs2375980

Variant names:

• chr9-2692622-C-G
• rs2375980
• XR_929436.3:n.1840G>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

Genes affected

LOC105375957 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LOC105375957	XR_929436.3	n.1840G>C		non_coding_transcript_exon_variant	Exon 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000286670	ENST00000768783.1	n.114-24561G>C		intron_variant	Intron 1 of 3
ENSG00000286670	ENST00000768784.1	n.157-24561G>C		intron_variant	Intron 1 of 3
ENSG00000286670	ENST00000768785.1	n.157-27547G>C		intron_variant	Intron 1 of 2

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

African (AFR) AF: 0.725 AC: 30038 AN: 41460

American (AMR) AF: 0.493 AC: 7530 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.475 AC: 1649 AN: 3468

East Asian (EAS) AF: 0.557 AC: 2886 AN: 5184

South Asian (SAS) AF: 0.450 AC: 2167 AN: 4818

European-Finnish (FIN) AF: 0.450 AC: 4754 AN: 10570

Middle Eastern (MID) AF: 0.442 AC: 130 AN: 294

European-Non Finnish (NFE) AF: 0.397 AC: 26959 AN: 67964

Other (OTH) AF: 0.458 AC: 969 AN: 2114

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
PhyloP100		-0.57

Splicing

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

Other links and lift over

dbSNP: rs2375980; hg19: chr9-2692622;