rs7323752

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105370102	XR_941720.2	n.106+7905A>G		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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 v4.3

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;