rs13027881

Variant names:

• chr2-6415801-G-A
• rs13027881
• XR_922743.1:n.133+3322C>T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The XR_922743.1(LOC105373402):​n.133+3322C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.115 in 152,154 control chromosomes in the GnomAD database, including 1,140 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 0.11 (1140 hom., cov: 32)
• Consequence: LOC105373402 XR_922743.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.38
• Publications: 4 publications found

Genes affected

LOC105373402 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.42).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.14 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: 0.115 AC: 17439 AN: 152036 Hom.: 1139 Cov.: 32

Gnomad AFR AF: 0.109

Gnomad AMI AF: 0.0965

Gnomad AMR AF: 0.0848

Gnomad ASJ AF: 0.0643

Gnomad EAS AF: 0.00695

Gnomad SAS AF: 0.0589

Gnomad FIN AF: 0.103

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.142

Gnomad OTH AF: 0.105

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

GnomAD4 genome AF: 0.115 AC: 17449 AN: 152154 Hom.: 1140 Cov.: 32 AF XY: 0.111 AC XY: 8232 AN XY: 74386

African (AFR) AF: 0.109 AC: 4537 AN: 41518

American (AMR) AF: 0.0846 AC: 1294 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0643 AC: 223 AN: 3470

East Asian (EAS) AF: 0.00696 AC: 36 AN: 5170

South Asian (SAS) AF: 0.0594 AC: 286 AN: 4816

European-Finnish (FIN) AF: 0.103 AC: 1088 AN: 10594

Middle Eastern (MID) AF: 0.0884 AC: 26 AN: 294

European-Non Finnish (NFE) AF: 0.142 AC: 9651 AN: 67970

Other (OTH) AF: 0.104 AC: 220 AN: 2114

Alfa AF: 0.127 Hom.: 1847

Bravo AF: 0.113

Asia WGS AF: 0.0440 AC: 155 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.42
CADD	Benign	15
DANN	Benign	0.53
PhyloP100		1.4

Splicing

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

Other links and lift over

dbSNP: rs13027881; hg19: chr2-6555933;