rs7187359

Variant names:

• chr16-30691834-G-A
• rs7187359

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 0.438 in 152,134 control chromosomes in the GnomAD database, including 20,141 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 0.44 (20141 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.167
• Publications: 20 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.844 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: 0.438 AC: 66561 AN: 152016 Hom.: 20099 Cov.: 32

Gnomad AFR AF: 0.851

Gnomad AMI AF: 0.418

Gnomad AMR AF: 0.279

Gnomad ASJ AF: 0.312

Gnomad EAS AF: 0.109

Gnomad SAS AF: 0.688

Gnomad FIN AF: 0.233

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.270

Gnomad OTH AF: 0.388

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

GnomAD4 genome AF: 0.438 AC: 66652 AN: 152134 Hom.: 20141 Cov.: 32 AF XY: 0.437 AC XY: 32461 AN XY: 74366

African (AFR) AF: 0.851 AC: 35330 AN: 41508

American (AMR) AF: 0.278 AC: 4249 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.312 AC: 1080 AN: 3464

East Asian (EAS) AF: 0.109 AC: 565 AN: 5186

South Asian (SAS) AF: 0.686 AC: 3310 AN: 4826

European-Finnish (FIN) AF: 0.233 AC: 2461 AN: 10570

Middle Eastern (MID) AF: 0.347 AC: 102 AN: 294

European-Non Finnish (NFE) AF: 0.270 AC: 18351 AN: 67980

Other (OTH) AF: 0.390 AC: 824 AN: 2114

Alfa AF: 0.334 Hom.: 6468

Bravo AF: 0.447

Asia WGS AF: 0.463 AC: 1608 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	3.6
DANN	Benign	0.38
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs7187359; hg19: chr16-30703155;