rs1875620

Variant names:

• chr9-88925144-G-A
• rs1875620
• XR_007061654.1:n.1967G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_007061654.1(LOC124902205):​n.1967G>A 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 0.436 in 152,112 control chromosomes in the GnomAD database, including 15,849 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 0.44 (15849 hom., cov: 34)
• Consequence: LOC124902205 XR_007061654.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.337
• Publications: 15 publications found

Genes affected

LOC124902205 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.547 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.436 AC: 66313 AN: 151994 Hom.: 15848 Cov.: 34

Gnomad AFR AF: 0.273

Gnomad AMI AF: 0.504

Gnomad AMR AF: 0.341

Gnomad ASJ AF: 0.450

Gnomad EAS AF: 0.241

Gnomad SAS AF: 0.468

Gnomad FIN AF: 0.550

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.552

Gnomad OTH AF: 0.412

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

GnomAD4 genome AF: 0.436 AC: 66315 AN: 152112 Hom.: 15849 Cov.: 34 AF XY: 0.431 AC XY: 32074 AN XY: 74392

African (AFR) AF: 0.272 AC: 11297 AN: 41498

American (AMR) AF: 0.340 AC: 5203 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.450 AC: 1561 AN: 3466

East Asian (EAS) AF: 0.241 AC: 1246 AN: 5174

South Asian (SAS) AF: 0.468 AC: 2254 AN: 4818

European-Finnish (FIN) AF: 0.550 AC: 5827 AN: 10596

Middle Eastern (MID) AF: 0.418 AC: 123 AN: 294

European-Non Finnish (NFE) AF: 0.552 AC: 37485 AN: 67942

Other (OTH) AF: 0.407 AC: 860 AN: 2114

Alfa AF: 0.503 Hom.: 70280

Bravo AF: 0.409

Asia WGS AF: 0.328 AC: 1140 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.38
DANN	Benign	0.44
PhyloP100		-0.34

Splicing

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

Other links and lift over

dbSNP: rs1875620; hg19: chr9-91540059;