rs7201099

chr16-55651764-T-Achr16-55651764-T-G

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 0.468 in 120,474 control chromosomes in the GnomAD database, including 12,129 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 0.47 (12129 hom., cov: 21)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.72

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.642 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: 0.468 AC: 56351 AN: 120370 Hom.: 12108 Cov.: 21

Gnomad AFR AF: 0.649

Gnomad AMI AF: 0.317

Gnomad AMR AF: 0.500

Gnomad ASJ AF: 0.347

Gnomad EAS AF: 0.460

Gnomad SAS AF: 0.348

Gnomad FIN AF: 0.413

Gnomad MID AF: 0.436

Gnomad NFE AF: 0.366

Gnomad OTH AF: 0.427

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

GnomAD4 genome AF: 0.468 AC: 56428 AN: 120474 Hom.: 12129 Cov.: 21 AF XY: 0.473 AC XY: 27385 AN XY: 57924

Gnomad4 AFR AF: 0.649

Gnomad4 AMR AF: 0.501

Gnomad4 ASJ AF: 0.347

Gnomad4 EAS AF: 0.459

Gnomad4 SAS AF: 0.349

Gnomad4 FIN AF: 0.413

Gnomad4 NFE AF: 0.366

Gnomad4 OTH AF: 0.429

Alfa AF: 0.151 Hom.: 220

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	0.68
Dann	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7201099; hg19: chr16-55685676;