chr13-20303727-A-G

Variant names:

• chr13-20303727-A-G
• rs7323769
• XR_941720.2:n.106+7934A>G

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+7934A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.396 in 152,022 control chromosomes in the GnomAD database, including 13,001 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 0.40 (13001 hom., cov: 32)
• Consequence: LOC105370102 XR_941720.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.945
• 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 (NFE) allele frequency at 95% confidence interval = 0.482 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: 0.397 AC: 60236 AN: 151904 Hom.: 12995 Cov.: 32

Gnomad AFR AF: 0.237

Gnomad AMI AF: 0.623

Gnomad AMR AF: 0.429

Gnomad ASJ AF: 0.337

Gnomad EAS AF: 0.236

Gnomad SAS AF: 0.410

Gnomad FIN AF: 0.472

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.487

Gnomad OTH AF: 0.379

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

GnomAD4 genome AF: 0.396 AC: 60270 AN: 152022 Hom.: 13001 Cov.: 32 AF XY: 0.394 AC XY: 29275 AN XY: 74302

African (AFR) AF: 0.237 AC: 9829 AN: 41484

American (AMR) AF: 0.429 AC: 6556 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.337 AC: 1170 AN: 3470

East Asian (EAS) AF: 0.236 AC: 1215 AN: 5154

South Asian (SAS) AF: 0.411 AC: 1977 AN: 4816

European-Finnish (FIN) AF: 0.472 AC: 4979 AN: 10554

Middle Eastern (MID) AF: 0.327 AC: 96 AN: 294

European-Non Finnish (NFE) AF: 0.487 AC: 33075 AN: 67966

Other (OTH) AF: 0.383 AC: 805 AN: 2104

Alfa AF: 0.448 Hom.: 29044

Bravo AF: 0.385

Asia WGS AF: 0.393 AC: 1368 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	0.35
DANN	Benign	0.23
PhyloP100		-0.94

Splicing

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

Other links and lift over

dbSNP: rs7323769; hg19: chr13-20877866;