13-97656387-G-A

Variant names:

• chr13-97656387-G-A
• rs1327918
• XR_007063845.1:n.2614+21404C>T

Variant summary

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

The XR_007063845.1(LOC105370324):​n.2614+21404C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.208 in 152,182 control chromosomes in the GnomAD database, including 4,220 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 0.21 (4220 hom., cov: 32)
• Consequence: LOC105370324 XR_007063845.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.614
• Publications: 2 publications found

Genes affected

LOC105370324 (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 (EAS) allele frequency at 95% confidence interval = 0.41 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: 0.208 AC: 31657 AN: 152064 Hom.: 4222 Cov.: 32

Gnomad AFR AF: 0.0519

Gnomad AMI AF: 0.253

Gnomad AMR AF: 0.299

Gnomad ASJ AF: 0.310

Gnomad EAS AF: 0.424

Gnomad SAS AF: 0.213

Gnomad FIN AF: 0.315

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.243

Gnomad OTH AF: 0.226

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

GnomAD4 genome AF: 0.208 AC: 31644 AN: 152182 Hom.: 4220 Cov.: 32 AF XY: 0.212 AC XY: 15795 AN XY: 74402

African (AFR) AF: 0.0518 AC: 2153 AN: 41538

American (AMR) AF: 0.298 AC: 4557 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.310 AC: 1075 AN: 3472

East Asian (EAS) AF: 0.424 AC: 2194 AN: 5170

South Asian (SAS) AF: 0.214 AC: 1030 AN: 4822

European-Finnish (FIN) AF: 0.315 AC: 3337 AN: 10592

Middle Eastern (MID) AF: 0.306 AC: 90 AN: 294

European-Non Finnish (NFE) AF: 0.243 AC: 16505 AN: 67990

Other (OTH) AF: 0.224 AC: 472 AN: 2108

Alfa AF: 0.235 Hom.: 10487

Bravo AF: 0.204

Asia WGS AF: 0.265 AC: 925 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	0.52
DANN	Benign	0.62
PhyloP100		-0.61

Splicing

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

Other links and lift over

dbSNP: rs1327918; hg19: chr13-98308641; COSMIC: COSV69618827;