rs932100

Variant names:

• chr4-107585427-A-G
• rs932100
• XR_939059.3:n.69+4902T>C

Variant summary

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

The XR_939059.3(LOC105377358):​n.69+4902T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.57 in 151,972 control chromosomes in the GnomAD database, including 24,818 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 0.57 (24818 hom., cov: 32)
• Consequence: LOC105377358 XR_939059.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.406
• Publications: 2 publications found

Genes affected

LOC105377358 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.619 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.570 AC: 86520 AN: 151854 Hom.: 24794 Cov.: 32

Gnomad AFR AF: 0.625

Gnomad AMI AF: 0.664

Gnomad AMR AF: 0.541

Gnomad ASJ AF: 0.556

Gnomad EAS AF: 0.385

Gnomad SAS AF: 0.445

Gnomad FIN AF: 0.613

Gnomad MID AF: 0.570

Gnomad NFE AF: 0.559

Gnomad OTH AF: 0.559

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

GnomAD4 genome AF: 0.570 AC: 86588 AN: 151972 Hom.: 24818 Cov.: 32 AF XY: 0.567 AC XY: 42086 AN XY: 74256

African (AFR) AF: 0.625 AC: 25894 AN: 41428

American (AMR) AF: 0.541 AC: 8259 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.556 AC: 1929 AN: 3470

East Asian (EAS) AF: 0.385 AC: 1996 AN: 5178

South Asian (SAS) AF: 0.443 AC: 2129 AN: 4808

European-Finnish (FIN) AF: 0.613 AC: 6447 AN: 10524

Middle Eastern (MID) AF: 0.585 AC: 172 AN: 294

European-Non Finnish (NFE) AF: 0.559 AC: 37979 AN: 67970

Other (OTH) AF: 0.558 AC: 1179 AN: 2112

Alfa AF: 0.558 Hom.: 98462

Bravo AF: 0.573

Asia WGS AF: 0.386 AC: 1343 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.9
DANN	Benign	0.67
PhyloP100		-0.41

Splicing

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

Other links and lift over

dbSNP: rs932100; hg19: chr4-108506584;