rs978714

chr13-105414824-A-Gchr13-105414824-A-T

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	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

Gnomad4 AFR AF: 0.307

Gnomad4 AMR AF: 0.493

Gnomad4 ASJ AF: 0.330

Gnomad4 EAS AF: 0.629

Gnomad4 SAS AF: 0.352

Gnomad4 FIN AF: 0.385

Gnomad4 NFE AF: 0.435

Gnomad4 OTH AF: 0.398

Alfa AF: 0.424 Hom.: 19635

Bravo AF: 0.410

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.57
Cadd	Benign	20
Dann	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs978714; hg19: chr13-106067173;