rs7983721

Variant names:

• chr13-42491096-G-A
• rs7983721

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 0.285 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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.354 AC: 14703 AN: 41498

American (AMR) AF: 0.377 AC: 5757 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.274 AC: 950 AN: 3470

East Asian (EAS) AF: 0.545 AC: 2819 AN: 5170

South Asian (SAS) AF: 0.207 AC: 998 AN: 4824

European-Finnish (FIN) AF: 0.165 AC: 1754 AN: 10602

Middle Eastern (MID) AF: 0.194 AC: 57 AN: 294

European-Non Finnish (NFE) AF: 0.229 AC: 15553 AN: 67996

Other (OTH) AF: 0.301 AC: 635 AN: 2112

Alfa AF: 0.273 Hom.: 1049

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
PhyloP100		1.0

Splicing

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

Other links and lift over

dbSNP: rs7983721; hg19: chr13-43065232;