chr13-105414824-A-G

Variant names:

• chr13-105414824-A-G
• rs978714

Variant summary

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

The variant allele was found at a frequency of 0.403 in 151,918 control chromosomes in the GnomAD database, including 12,856 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 (12856 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.30
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.57).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.611 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.403 AC: 61147 AN: 151800 Hom.: 12854 Cov.: 33

Gnomad AFR AF: 0.308

Gnomad AMI AF: 0.280

Gnomad AMR AF: 0.492

Gnomad ASJ AF: 0.330

Gnomad EAS AF: 0.629

Gnomad SAS AF: 0.353

Gnomad FIN AF: 0.385

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.435

Gnomad OTH AF: 0.397

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

GnomAD4 genome AF: 0.403 AC: 61159 AN: 151918 Hom.: 12856 Cov.: 33 AF XY: 0.402 AC XY: 29843 AN XY: 74270

African (AFR) AF: 0.307 AC: 12748 AN: 41464

American (AMR) AF: 0.493 AC: 7523 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.330 AC: 1144 AN: 3466

East Asian (EAS) AF: 0.629 AC: 3257 AN: 5176

South Asian (SAS) AF: 0.352 AC: 1697 AN: 4820

European-Finnish (FIN) AF: 0.385 AC: 4070 AN: 10560

Middle Eastern (MID) AF: 0.354 AC: 104 AN: 294

European-Non Finnish (NFE) AF: 0.435 AC: 29522 AN: 67864

Other (OTH) AF: 0.398 AC: 840 AN: 2112

Alfa AF: 0.425 Hom.: 25634

Bravo AF: 0.410

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.57
CADD	Benign	20
DANN	Benign	0.79
PhyloP100		2.3

Splicing

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

Other links and lift over

dbSNP: rs978714; hg19: chr13-106067173;