16-19962546-A-G

Variant names:

• chr16-19962546-A-G
• rs7187990

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 0.537 in 151,432 control chromosomes in the GnomAD database, including 24,520 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 0.54 (24520 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.843
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.813 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: 0.537 AC: 81242 AN: 151314 Hom.: 24468 Cov.: 28

Gnomad AFR AF: 0.821

Gnomad AMI AF: 0.238

Gnomad AMR AF: 0.432

Gnomad ASJ AF: 0.451

Gnomad EAS AF: 0.679

Gnomad SAS AF: 0.564

Gnomad FIN AF: 0.425

Gnomad MID AF: 0.382

Gnomad NFE AF: 0.403

Gnomad OTH AF: 0.500

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

GnomAD4 genome AF: 0.537 AC: 81348 AN: 151432 Hom.: 24520 Cov.: 28 AF XY: 0.537 AC XY: 39670 AN XY: 73942

African (AFR) AF: 0.821 AC: 33860 AN: 41258

American (AMR) AF: 0.431 AC: 6547 AN: 15198

Ashkenazi Jewish (ASJ) AF: 0.451 AC: 1558 AN: 3458

East Asian (EAS) AF: 0.680 AC: 3474 AN: 5110

South Asian (SAS) AF: 0.564 AC: 2695 AN: 4776

European-Finnish (FIN) AF: 0.425 AC: 4438 AN: 10454

Middle Eastern (MID) AF: 0.394 AC: 115 AN: 292

European-Non Finnish (NFE) AF: 0.403 AC: 27382 AN: 67876

Other (OTH) AF: 0.506 AC: 1063 AN: 2102

Alfa AF: 0.534 Hom.: 16133

Bravo AF: 0.549

Asia WGS AF: 0.663 AC: 2305 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.22
DANN	Benign	0.36
PhyloP100		-0.84

Splicing

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

Other links and lift over

dbSNP: rs7187990; hg19: chr16-19973868;