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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124902205	XR_007061654.1	n.1967G>A		non_coding_transcript_exon_variant	Exon 4 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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 v4.3

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;