rs16944

Variant names:

• chr2-112837290-A-G
• rs16944

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

Feb 11, 2020

HLA Laboratory, Instituto Nacional de Enfermedades Respiratorias Ismael Cosio Villegas

Significance: association

Review Status: no assertion criteria provided

Collection Method: case-control

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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;