rs7201408

Variant names:

• chr16-20082732-A-G
• rs7201408

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 0.25 in 151,826 control chromosomes in the GnomAD database, including 4,798 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 0.25 (4798 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.483
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.256 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: 0.250 AC: 37984 AN: 151708 Hom.: 4798 Cov.: 30

Gnomad AFR AF: 0.242

Gnomad AMI AF: 0.400

Gnomad AMR AF: 0.246

Gnomad ASJ AF: 0.208

Gnomad EAS AF: 0.268

Gnomad SAS AF: 0.233

Gnomad FIN AF: 0.299

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.249

Gnomad OTH AF: 0.234

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

GnomAD4 genome AF: 0.250 AC: 38020 AN: 151826 Hom.: 4798 Cov.: 30 AF XY: 0.252 AC XY: 18701 AN XY: 74176

African (AFR) AF: 0.243 AC: 10055 AN: 41402

American (AMR) AF: 0.247 AC: 3761 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.208 AC: 720 AN: 3468

East Asian (EAS) AF: 0.268 AC: 1376 AN: 5138

South Asian (SAS) AF: 0.232 AC: 1116 AN: 4802

European-Finnish (FIN) AF: 0.299 AC: 3155 AN: 10548

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.249 AC: 16933 AN: 67906

Other (OTH) AF: 0.231 AC: 487 AN: 2106

Alfa AF: 0.249 Hom.: 2916

Bravo AF: 0.249

Asia WGS AF: 0.243 AC: 843 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.0
DANN	Benign	0.48
PhyloP100		-0.48

Splicing

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

Other links and lift over

dbSNP: rs7201408; hg19: chr16-20094054;