rs16944

Positions:

• chr2-112837290-A-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 0.573 in 152,000 control chromosomes in the GnomAD database, including 25,795 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as association (no stars).

• Frequency: Genomes: 𝑓 0.57 (25795 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: association no assertion criteria provided O:1
• Conservation: PhyloP100: -0.560

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.661 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.574 AC: 87133 AN: 151882 Hom.: 25788 Cov.: 32

Gnomad AFR AF: 0.456

Gnomad AMI AF: 0.736

Gnomad AMR AF: 0.500

Gnomad ASJ AF: 0.651

Gnomad EAS AF: 0.537

Gnomad SAS AF: 0.406

Gnomad FIN AF: 0.597

Gnomad MID AF: 0.653

Gnomad NFE AF: 0.666

Gnomad OTH AF: 0.587

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

GnomAD4 genome AF: 0.573 AC: 87156 AN: 152000 Hom.: 25795 Cov.: 32 AF XY: 0.566 AC XY: 42063 AN XY: 74286

Gnomad4 AFR AF: 0.456

Gnomad4 AMR AF: 0.499

Gnomad4 ASJ AF: 0.651

Gnomad4 EAS AF: 0.537

Gnomad4 SAS AF: 0.405

Gnomad4 FIN AF: 0.597

Gnomad4 NFE AF: 0.666

Gnomad4 OTH AF: 0.582

Alfa AF: 0.643 Hom.: 37635

Bravo AF: 0.564

Asia WGS AF: 0.456 AC: 1587 AN: 3478

ClinVar

Significance: association

Submissions summary: Other:1

Revision: no assertion criteria provided

Submissions by phenotype

Antisynthetase syndrome Other:1

association, no assertion criteria provided

case-control

HLA Laboratory, Instituto Nacional de Enfermedades Respiratorias Ismael Cosio Villegas

Feb 11, 2020

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.38
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16944; hg19: chr2-113594867;