rs978714

Variant names:

• chr13-105414824-A-G
• rs978714

Your query was ambiguous. Multiple possible variants found:

• chr13-105414824-A-G
• chr13-105414824-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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;