rs7984003

Positions:

• chr13-82292438-T-C

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 0.857 in 152,174 control chromosomes in the GnomAD database, including 56,173 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 0.86 (56173 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.05

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.934 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: 0.857 AC: 130278 AN: 152056 Hom.: 56110 Cov.: 32

Gnomad AFR AF: 0.942

Gnomad AMI AF: 0.782

Gnomad AMR AF: 0.852

Gnomad ASJ AF: 0.815

Gnomad EAS AF: 0.943

Gnomad SAS AF: 0.859

Gnomad FIN AF: 0.768

Gnomad MID AF: 0.832

Gnomad NFE AF: 0.816

Gnomad OTH AF: 0.854

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

GnomAD4 genome AF: 0.857 AC: 130401 AN: 152174 Hom.: 56173 Cov.: 32 AF XY: 0.856 AC XY: 63700 AN XY: 74386

Gnomad4 AFR AF: 0.942

Gnomad4 AMR AF: 0.853

Gnomad4 ASJ AF: 0.815

Gnomad4 EAS AF: 0.943

Gnomad4 SAS AF: 0.858

Gnomad4 FIN AF: 0.768

Gnomad4 NFE AF: 0.816

Gnomad4 OTH AF: 0.855

Alfa AF: 0.826 Hom.: 68514

Bravo AF: 0.869

Asia WGS AF: 0.919 AC: 3195 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.3
DANN	Benign	0.27

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7984003; hg19: chr13-82866573;