rs3936010

Variant names:

• chr4-107566701-G-C
• rs3936010
• XR_939059.3:n.130+12308C>G

Variant summary

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

The XR_939059.3(LOC105377358):​n.130+12308C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.02 in 152,230 control chromosomes in the GnomAD database, including 81 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 0.020 (81 hom., cov: 32)
• Consequence: LOC105377358 XR_939059.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.289
• 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=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0966 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: 0.0200 AC: 3049 AN: 152112 Hom.: 81 Cov.: 32

Gnomad AFR AF: 0.00531

Gnomad AMI AF: 0.0417

Gnomad AMR AF: 0.0335

Gnomad ASJ AF: 0.00835

Gnomad EAS AF: 0.104

Gnomad SAS AF: 0.0108

Gnomad FIN AF: 0.0176

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0211

Gnomad OTH AF: 0.0181

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

GnomAD4 genome AF: 0.0200 AC: 3047 AN: 152230 Hom.: 81 Cov.: 32 AF XY: 0.0202 AC XY: 1506 AN XY: 74424

African (AFR) AF: 0.00530 AC: 220 AN: 41540

American (AMR) AF: 0.0335 AC: 512 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.00835 AC: 29 AN: 3472

East Asian (EAS) AF: 0.104 AC: 537 AN: 5168

South Asian (SAS) AF: 0.0108 AC: 52 AN: 4824

European-Finnish (FIN) AF: 0.0176 AC: 187 AN: 10606

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.0211 AC: 1434 AN: 68024

Other (OTH) AF: 0.0180 AC: 38 AN: 2116

Alfa AF: 0.0184 Hom.: 6

Bravo AF: 0.0254

Asia WGS AF: 0.0420 AC: 146 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.49
DANN	Benign	0.61
PhyloP100		-0.29

Splicing

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

Other links and lift over

dbSNP: rs3936010; hg19: chr4-108487858;