rs1879908

Variant names:

• chr4-180920703-C-A
• rs1879908
• XR_007058399.1:n.205+933G>T

Your query was ambiguous. Multiple possible variants found:

• chr4-180920703-C-A
• chr4-180920703-C-G

Variant summary

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

The XR_007058399.1(LOC124900821):​n.205+933G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.889 in 152,202 control chromosomes in the GnomAD database, including 60,767 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 0.89 (60767 hom., cov: 32)
• Consequence: LOC124900821 XR_007058399.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.05
• Publications: 1 publications found

Genes affected

LOC124900821 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.973 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: 0.890 AC: 135304 AN: 152084 Hom.: 60738 Cov.: 32

Gnomad AFR AF: 0.748

Gnomad AMI AF: 0.964

Gnomad AMR AF: 0.936

Gnomad ASJ AF: 0.974

Gnomad EAS AF: 0.996

Gnomad SAS AF: 0.967

Gnomad FIN AF: 0.962

Gnomad MID AF: 0.962

Gnomad NFE AF: 0.934

Gnomad OTH AF: 0.925

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

GnomAD4 genome AF: 0.889 AC: 135381 AN: 152202 Hom.: 60767 Cov.: 32 AF XY: 0.895 AC XY: 66564 AN XY: 74410

African (AFR) AF: 0.747 AC: 31007 AN: 41490

American (AMR) AF: 0.936 AC: 14317 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.974 AC: 3379 AN: 3468

East Asian (EAS) AF: 0.996 AC: 5152 AN: 5172

South Asian (SAS) AF: 0.968 AC: 4673 AN: 4828

European-Finnish (FIN) AF: 0.962 AC: 10210 AN: 10608

Middle Eastern (MID) AF: 0.966 AC: 284 AN: 294

European-Non Finnish (NFE) AF: 0.934 AC: 63524 AN: 68024

Other (OTH) AF: 0.925 AC: 1956 AN: 2114

Alfa AF: 0.905 Hom.: 7767

Bravo AF: 0.884

Asia WGS AF: 0.948 AC: 3297 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.15
DANN	Benign	0.47
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs1879908; hg19: chr4-181841856;