rs7201099

Variant names:

• chr16-55651764-T-A
• rs7201099

Your query was ambiguous. Multiple possible variants found:

• chr16-55651764-T-A
• chr16-55651764-T-G

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 0.468 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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.649 AC: 23003 AN: 35440

American (AMR) AF: 0.501 AC: 6032 AN: 12040

Ashkenazi Jewish (ASJ) AF: 0.347 AC: 945 AN: 2722

East Asian (EAS) AF: 0.459 AC: 1922 AN: 4188

South Asian (SAS) AF: 0.349 AC: 1242 AN: 3556

European-Finnish (FIN) AF: 0.413 AC: 2750 AN: 6658

Middle Eastern (MID) AF: 0.444 AC: 88 AN: 198

European-Non Finnish (NFE) AF: 0.366 AC: 19544 AN: 53420

Other (OTH) AF: 0.429 AC: 722 AN: 1684

Alfa AF: 0.151 Hom.: 220

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.68
DANN	Benign	0.51
PhyloP100		-2.7

Splicing

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

Other links and lift over

dbSNP: rs7201099; hg19: chr16-55685676;