rs4751808

Variant names:

• chr10-120917550-A-G
• rs4751808
• XR_001747609.2:n.541-15208T>C

Variant summary

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

The XR_946372.3(LOC105378519):​n.226+8738T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.651 in 152,180 control chromosomes in the GnomAD database, including 33,105 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 0.65 (33105 hom., cov: 34)
• Consequence: LOC105378519 XR_946372.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00300
• Publications: 6 publications found

Genes affected

LOC105378519 (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 (AFR) allele frequency at 95% confidence interval = 0.808 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: 0.650 AC: 98914 AN: 152060 Hom.: 33050 Cov.: 34

Gnomad AFR AF: 0.815

Gnomad AMI AF: 0.698

Gnomad AMR AF: 0.639

Gnomad ASJ AF: 0.680

Gnomad EAS AF: 0.518

Gnomad SAS AF: 0.576

Gnomad FIN AF: 0.518

Gnomad MID AF: 0.604

Gnomad NFE AF: 0.587

Gnomad OTH AF: 0.646

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

GnomAD4 genome AF: 0.651 AC: 99023 AN: 152180 Hom.: 33105 Cov.: 34 AF XY: 0.643 AC XY: 47810 AN XY: 74396

African (AFR) AF: 0.815 AC: 33862 AN: 41546

American (AMR) AF: 0.639 AC: 9765 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.680 AC: 2358 AN: 3468

East Asian (EAS) AF: 0.518 AC: 2675 AN: 5164

South Asian (SAS) AF: 0.575 AC: 2778 AN: 4828

European-Finnish (FIN) AF: 0.518 AC: 5481 AN: 10584

Middle Eastern (MID) AF: 0.602 AC: 177 AN: 294

European-Non Finnish (NFE) AF: 0.587 AC: 39922 AN: 67980

Other (OTH) AF: 0.647 AC: 1370 AN: 2116

Alfa AF: 0.610 Hom.: 112973

Bravo AF: 0.668

Asia WGS AF: 0.560 AC: 1949 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.9
DANN	Benign	0.58
PhyloP100		0.0030

Splicing

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

Other links and lift over

dbSNP: rs4751808; hg19: chr10-122677062;