13-20297156-G-A

Variant names:

• chr13-20297156-G-A
• rs7327522
• XR_941720.2:n.106+1363G>A

Variant summary

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

The XR_941720.2(LOC105370102):​n.106+1363G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.659 in 151,592 control chromosomes in the GnomAD database, including 33,658 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 (33658 hom., cov: 30)
• Consequence: LOC105370102 XR_941720.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.385
• Publications: 4 publications found

Genes affected

LOC105370102 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.759 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.659 AC: 99752 AN: 151474 Hom.: 33637 Cov.: 30

Gnomad AFR AF: 0.767

Gnomad AMI AF: 0.590

Gnomad AMR AF: 0.718

Gnomad ASJ AF: 0.666

Gnomad EAS AF: 0.296

Gnomad SAS AF: 0.620

Gnomad FIN AF: 0.619

Gnomad MID AF: 0.661

Gnomad NFE AF: 0.616

Gnomad OTH AF: 0.657

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

GnomAD4 genome AF: 0.659 AC: 99826 AN: 151592 Hom.: 33658 Cov.: 30 AF XY: 0.657 AC XY: 48642 AN XY: 74046

African (AFR) AF: 0.767 AC: 31701 AN: 41356

American (AMR) AF: 0.718 AC: 10942 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.666 AC: 2308 AN: 3466

East Asian (EAS) AF: 0.295 AC: 1511 AN: 5116

South Asian (SAS) AF: 0.620 AC: 2985 AN: 4814

European-Finnish (FIN) AF: 0.619 AC: 6478 AN: 10462

Middle Eastern (MID) AF: 0.650 AC: 191 AN: 294

European-Non Finnish (NFE) AF: 0.616 AC: 41795 AN: 67836

Other (OTH) AF: 0.658 AC: 1386 AN: 2106

Alfa AF: 0.644 Hom.: 68482

Bravo AF: 0.672

Asia WGS AF: 0.531 AC: 1846 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	4.4
DANN	Benign	0.81
PhyloP100		0.39

Splicing

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

Other links and lift over

dbSNP: rs7327522; hg19: chr13-20871295;