rs7722413

Variant names:

• chr5-138942562-T-C
• rs7722413

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 0.352 in 152,054 control chromosomes in the GnomAD database, including 10,339 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 0.35 (10339 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.668
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.06).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.519 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: 0.352 AC: 53523 AN: 151936 Hom.: 10318 Cov.: 32

Gnomad AFR AF: 0.525

Gnomad AMI AF: 0.315

Gnomad AMR AF: 0.263

Gnomad ASJ AF: 0.341

Gnomad EAS AF: 0.0491

Gnomad SAS AF: 0.274

Gnomad FIN AF: 0.295

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.307

Gnomad OTH AF: 0.316

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

GnomAD4 genome AF: 0.352 AC: 53586 AN: 152054 Hom.: 10339 Cov.: 32 AF XY: 0.347 AC XY: 25822 AN XY: 74336

African (AFR) AF: 0.525 AC: 21767 AN: 41454

American (AMR) AF: 0.263 AC: 4016 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.341 AC: 1183 AN: 3470

East Asian (EAS) AF: 0.0491 AC: 254 AN: 5178

South Asian (SAS) AF: 0.273 AC: 1315 AN: 4820

European-Finnish (FIN) AF: 0.295 AC: 3120 AN: 10566

Middle Eastern (MID) AF: 0.350 AC: 103 AN: 294

European-Non Finnish (NFE) AF: 0.307 AC: 20883 AN: 67970

Other (OTH) AF: 0.312 AC: 658 AN: 2108

Alfa AF: 0.314 Hom.: 12714

Bravo AF: 0.355

Asia WGS AF: 0.163 AC: 568 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.16
DANN	Benign	0.17
PhyloP100		-0.67

Splicing

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

Other links and lift over

dbSNP: rs7722413; hg19: chr5-138278251; COSMIC: COSV54529912;