rs7721882

Variant names:

• chr5-132083255-A-G
• rs7721882

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 0.326 in 151,970 control chromosomes in the GnomAD database, including 9,015 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 0.33 (9015 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.150
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.418 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: 0.326 AC: 49540 AN: 151852 Hom.: 9012 Cov.: 32

Gnomad AFR AF: 0.242

Gnomad AMI AF: 0.595

Gnomad AMR AF: 0.324

Gnomad ASJ AF: 0.332

Gnomad EAS AF: 0.00329

Gnomad SAS AF: 0.112

Gnomad FIN AF: 0.269

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.422

Gnomad OTH AF: 0.368

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

GnomAD4 genome AF: 0.326 AC: 49556 AN: 151970 Hom.: 9015 Cov.: 32 AF XY: 0.311 AC XY: 23110 AN XY: 74256

African (AFR) AF: 0.242 AC: 10031 AN: 41448

American (AMR) AF: 0.324 AC: 4942 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.332 AC: 1152 AN: 3466

East Asian (EAS) AF: 0.00330 AC: 17 AN: 5156

South Asian (SAS) AF: 0.112 AC: 539 AN: 4810

European-Finnish (FIN) AF: 0.269 AC: 2836 AN: 10562

Middle Eastern (MID) AF: 0.296 AC: 87 AN: 294

European-Non Finnish (NFE) AF: 0.422 AC: 28645 AN: 67940

Other (OTH) AF: 0.363 AC: 767 AN: 2112

Alfa AF: 0.358 Hom.: 1258

Bravo AF: 0.331

Asia WGS AF: 0.0660 AC: 230 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	7.6
DANN	Benign	0.86
PhyloP100		0.15

Splicing

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

Other links and lift over

dbSNP: rs7721882; hg19: chr5-131418948; COSMIC: COSV72770489;