XR_941720.2:n.106+7905A>G

Variant names:

• chr13-20303698-A-G
• rs7323752
• XR_941720.2:n.106+7905A>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+7905A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.559 in 151,966 control chromosomes in the GnomAD database, including 24,330 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 0.56 (24330 hom., cov: 32)
• Consequence: LOC105370102 XR_941720.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.158
• Publications: 1 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=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.631 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: 0.559 AC: 84870 AN: 151848 Hom.: 24297 Cov.: 32

Gnomad AFR AF: 0.637

Gnomad AMI AF: 0.637

Gnomad AMR AF: 0.544

Gnomad ASJ AF: 0.483

Gnomad EAS AF: 0.236

Gnomad SAS AF: 0.481

Gnomad FIN AF: 0.493

Gnomad MID AF: 0.491

Gnomad NFE AF: 0.558

Gnomad OTH AF: 0.553

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

GnomAD4 genome AF: 0.559 AC: 84963 AN: 151966 Hom.: 24330 Cov.: 32 AF XY: 0.552 AC XY: 40972 AN XY: 74280

African (AFR) AF: 0.637 AC: 26391 AN: 41430

American (AMR) AF: 0.544 AC: 8317 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.483 AC: 1673 AN: 3466

East Asian (EAS) AF: 0.236 AC: 1211 AN: 5138

South Asian (SAS) AF: 0.483 AC: 2327 AN: 4820

European-Finnish (FIN) AF: 0.493 AC: 5202 AN: 10560

Middle Eastern (MID) AF: 0.500 AC: 147 AN: 294

European-Non Finnish (NFE) AF: 0.558 AC: 37944 AN: 67958

Other (OTH) AF: 0.556 AC: 1171 AN: 2108

Alfa AF: 0.553 Hom.: 46243

Bravo AF: 0.566

Asia WGS AF: 0.452 AC: 1573 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	3.6
DANN	Benign	0.38
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs7323752; hg19: chr13-20877837;