13-62862667-A-G

Variant names:

• chr13-62862667-A-G
• rs2204037
• XR_942013.2:n.292-23414T>C

Variant summary

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

The XR_942013.2(LOC105370234):​n.292-23414T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.657 in 152,036 control chromosomes in the GnomAD database, including 33,175 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 0.66 (33175 hom., cov: 32)
• Consequence: LOC105370234 XR_942013.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.26
• Publications: 7 publications found

Genes affected

LOC105370234 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.823 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: 0.657 AC: 99787 AN: 151918 Hom.: 33158 Cov.: 32

Gnomad AFR AF: 0.648

Gnomad AMI AF: 0.456

Gnomad AMR AF: 0.741

Gnomad ASJ AF: 0.617

Gnomad EAS AF: 0.844

Gnomad SAS AF: 0.709

Gnomad FIN AF: 0.740

Gnomad MID AF: 0.703

Gnomad NFE AF: 0.617

Gnomad OTH AF: 0.669

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

GnomAD4 genome AF: 0.657 AC: 99858 AN: 152036 Hom.: 33175 Cov.: 32 AF XY: 0.667 AC XY: 49556 AN XY: 74288

African (AFR) AF: 0.648 AC: 26863 AN: 41470

American (AMR) AF: 0.741 AC: 11321 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.617 AC: 2142 AN: 3472

East Asian (EAS) AF: 0.844 AC: 4343 AN: 5144

South Asian (SAS) AF: 0.709 AC: 3425 AN: 4830

European-Finnish (FIN) AF: 0.740 AC: 7816 AN: 10564

Middle Eastern (MID) AF: 0.687 AC: 202 AN: 294

European-Non Finnish (NFE) AF: 0.617 AC: 41917 AN: 67970

Other (OTH) AF: 0.671 AC: 1414 AN: 2106

Alfa AF: 0.629 Hom.: 127002

Bravo AF: 0.657

Asia WGS AF: 0.764 AC: 2656 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.84
DANN	Benign	0.38
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs2204037; hg19: chr13-63436800; COSMIC: COSV69356737;