4-180916588-C-T

Variant names:

• chr4-180916588-C-T
• rs6848893
• XR_001741481.2:n.163+1197G>A

Variant summary

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

The XR_001741481.2(LOC105377568):​n.163+1197G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.901 in 152,118 control chromosomes in the GnomAD database, including 62,107 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 0.90 (62107 hom., cov: 31)
• Consequence: LOC105377568 XR_001741481.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.99
• Publications: 6 publications found

Genes affected

LOC105377568 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.974 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: 0.901 AC: 136935 AN: 152000 Hom.: 62077 Cov.: 31

Gnomad AFR AF: 0.779

Gnomad AMI AF: 0.964

Gnomad AMR AF: 0.944

Gnomad ASJ AF: 0.976

Gnomad EAS AF: 0.996

Gnomad SAS AF: 0.971

Gnomad FIN AF: 0.965

Gnomad MID AF: 0.965

Gnomad NFE AF: 0.937

Gnomad OTH AF: 0.932

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

GnomAD4 genome AF: 0.901 AC: 137013 AN: 152118 Hom.: 62107 Cov.: 31 AF XY: 0.905 AC XY: 67305 AN XY: 74362

African (AFR) AF: 0.778 AC: 32252 AN: 41450

American (AMR) AF: 0.944 AC: 14429 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.976 AC: 3386 AN: 3470

East Asian (EAS) AF: 0.996 AC: 5143 AN: 5162

South Asian (SAS) AF: 0.971 AC: 4676 AN: 4816

European-Finnish (FIN) AF: 0.965 AC: 10235 AN: 10602

Middle Eastern (MID) AF: 0.969 AC: 285 AN: 294

European-Non Finnish (NFE) AF: 0.937 AC: 63757 AN: 68012

Other (OTH) AF: 0.932 AC: 1971 AN: 2114

Alfa AF: 0.898 Hom.: 3291

Bravo AF: 0.896

Asia WGS AF: 0.947 AC: 3296 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.026
DANN	Benign	0.54
PhyloP100		-3.0

Splicing

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

Other links and lift over

dbSNP: rs6848893; hg19: chr4-181837741;