rs7984003

Variant names:

• chr13-82292438-T-C
• rs7984003

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 0.857 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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.942 AC: 39142 AN: 41550

American (AMR) AF: 0.853 AC: 13031 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.815 AC: 2827 AN: 3470

East Asian (EAS) AF: 0.943 AC: 4850 AN: 5142

South Asian (SAS) AF: 0.858 AC: 4144 AN: 4830

European-Finnish (FIN) AF: 0.768 AC: 8122 AN: 10578

Middle Eastern (MID) AF: 0.847 AC: 249 AN: 294

European-Non Finnish (NFE) AF: 0.816 AC: 55520 AN: 68006

Other (OTH) AF: 0.855 AC: 1803 AN: 2108

Alfa AF: 0.830 Hom.: 87453

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
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs7984003; hg19: chr13-82866573;