rs7983721

chr13-42491096-G-A

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 0.285 in 152,168 control chromosomes in the GnomAD database, including 6,864 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 0.29 (6864 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.00

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.528 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: 0.285 AC: 43364 AN: 152050 Hom.: 6854 Cov.: 33

Gnomad AFR AF: 0.354

Gnomad AMI AF: 0.204

Gnomad AMR AF: 0.376

Gnomad ASJ AF: 0.274

Gnomad EAS AF: 0.546

Gnomad SAS AF: 0.207

Gnomad FIN AF: 0.165

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.229

Gnomad OTH AF: 0.304

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

GnomAD4 genome AF: 0.285 AC: 43412 AN: 152168 Hom.: 6864 Cov.: 33 AF XY: 0.284 AC XY: 21112 AN XY: 74380

Gnomad4 AFR AF: 0.354

Gnomad4 AMR AF: 0.377

Gnomad4 ASJ AF: 0.274

Gnomad4 EAS AF: 0.545

Gnomad4 SAS AF: 0.207

Gnomad4 FIN AF: 0.165

Gnomad4 NFE AF: 0.229

Gnomad4 OTH AF: 0.301

Alfa AF: 0.270 Hom.: 997

Bravo AF: 0.309

Asia WGS AF: 0.343 AC: 1192 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
Cadd	Benign	6.4
Dann	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7983721; hg19: chr13-43065232;