XR_941720.2:n.201-1593G>C

Variant names:

• chr13-20323772-G-C
• rs7337318
• XR_941720.2:n.201-1593G>C

Variant summary

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

The XR_941720.2(LOC105370102):​n.201-1593G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.554 in 151,848 control chromosomes in the GnomAD database, including 23,622 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 0.55 (23622 hom., cov: 31)
• Consequence: LOC105370102 XR_941720.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.02
• Publications: 0 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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.585 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: 0.554 AC: 84058 AN: 151730 Hom.: 23594 Cov.: 31

Gnomad AFR AF: 0.551

Gnomad AMI AF: 0.616

Gnomad AMR AF: 0.540

Gnomad ASJ AF: 0.527

Gnomad EAS AF: 0.249

Gnomad SAS AF: 0.538

Gnomad FIN AF: 0.513

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.590

Gnomad OTH AF: 0.559

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

GnomAD4 genome AF: 0.554 AC: 84145 AN: 151848 Hom.: 23622 Cov.: 31 AF XY: 0.547 AC XY: 40582 AN XY: 74226

African (AFR) AF: 0.551 AC: 22802 AN: 41352

American (AMR) AF: 0.540 AC: 8245 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.527 AC: 1829 AN: 3470

East Asian (EAS) AF: 0.248 AC: 1279 AN: 5152

South Asian (SAS) AF: 0.540 AC: 2600 AN: 4818

European-Finnish (FIN) AF: 0.513 AC: 5411 AN: 10552

Middle Eastern (MID) AF: 0.537 AC: 158 AN: 294

European-Non Finnish (NFE) AF: 0.590 AC: 40076 AN: 67926

Other (OTH) AF: 0.562 AC: 1184 AN: 2108

Alfa AF: 0.568 Hom.: 3048

Bravo AF: 0.553

Asia WGS AF: 0.467 AC: 1627 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.032
DANN	Benign	0.57
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs7337318; hg19: chr13-20897911;