rs16944

Variant names:

• chr2-112837290-A-G
• rs16944
• ENST00000762706.1:n.405-47968A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000762706.1(ENSG00000299339):​n.405-47968A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. 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: ENSG00000299339 ENST00000762706.1 intron
• Clinical Significance: association no assertion criteria provided O:1
• Conservation: PhyloP100: -0.560
• Publications: 934 publications found

Genes affected

ENSG00000299339 (HGNC:):

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 (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
ENSG00000299339	ENST00000762706.1	n.405-47968A>G		intron_variant	Intron 2 of 3
ENSG00000299339	ENST00000762707.1	n.500-47968A>G		intron_variant	Intron 2 of 2
ENSG00000299339	ENST00000762708.1	n.266-47968A>G		intron_variant	Intron 2 of 2

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

African (AFR) AF: 0.456 AC: 18878 AN: 41422

American (AMR) AF: 0.499 AC: 7613 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.651 AC: 2262 AN: 3472

East Asian (EAS) AF: 0.537 AC: 2757 AN: 5130

South Asian (SAS) AF: 0.405 AC: 1953 AN: 4822

European-Finnish (FIN) AF: 0.597 AC: 6317 AN: 10582

Middle Eastern (MID) AF: 0.668 AC: 195 AN: 292

European-Non Finnish (NFE) AF: 0.666 AC: 45280 AN: 67984

Other (OTH) AF: 0.582 AC: 1230 AN: 2114

Alfa AF: 0.631 Hom.: 90946

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

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.38
DANN	Benign	0.44
PhyloP100		-0.56
PromoterAI		-0.019	Neutral

Splicing

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

Other links and lift over

dbSNP: rs16944; hg19: chr2-113594867;