rs4811626

Variant names:

• chr20-55804087-T-C
• rs4811626
• XR_936887.2:n.83+105T>C

Variant summary

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

The XR_936887.2(LOC105372677):​n.83+105T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.653 in 151,802 control chromosomes in the GnomAD database, including 34,000 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 (34000 hom., cov: 31)
• Consequence: LOC105372677 XR_936887.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.578
• Publications: 2 publications found

Genes affected

LOC105372677 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.872 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: 0.652 AC: 98961 AN: 151684 Hom.: 33936 Cov.: 31

Gnomad AFR AF: 0.879

Gnomad AMI AF: 0.534

Gnomad AMR AF: 0.596

Gnomad ASJ AF: 0.548

Gnomad EAS AF: 0.469

Gnomad SAS AF: 0.598

Gnomad FIN AF: 0.549

Gnomad MID AF: 0.548

Gnomad NFE AF: 0.569

Gnomad OTH AF: 0.621

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

GnomAD4 genome AF: 0.653 AC: 99085 AN: 151802 Hom.: 34000 Cov.: 31 AF XY: 0.649 AC XY: 48102 AN XY: 74166

African (AFR) AF: 0.879 AC: 36455 AN: 41454

American (AMR) AF: 0.596 AC: 9066 AN: 15202

Ashkenazi Jewish (ASJ) AF: 0.548 AC: 1901 AN: 3468

East Asian (EAS) AF: 0.469 AC: 2393 AN: 5102

South Asian (SAS) AF: 0.598 AC: 2876 AN: 4812

European-Finnish (FIN) AF: 0.549 AC: 5764 AN: 10494

Middle Eastern (MID) AF: 0.548 AC: 160 AN: 292

European-Non Finnish (NFE) AF: 0.569 AC: 38677 AN: 67962

Other (OTH) AF: 0.621 AC: 1306 AN: 2104

Alfa AF: 0.592 Hom.: 45226

Bravo AF: 0.665

Asia WGS AF: 0.541 AC: 1883 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	10
DANN	Benign	0.40
PhyloP100		0.58

Splicing

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

Other links and lift over

dbSNP: rs4811626; hg19: chr20-54379143;