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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105372677	XR_936887.2	n.83+105T>C		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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 v4.3

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;