rs9938149

Variant names:

• chr16-88298034-C-A
• rs9938149
• XM_047434810.1:c.-192+21459C>A

Your query was ambiguous. Multiple possible variants found:

• chr16-88298034-C-A
• chr16-88298034-C-G
• chr16-88298034-C-T

Variant summary

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

The ENST00000563190.1(LINC02182):​n.344+3193C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.664 in 152,030 control chromosomes in the GnomAD database, including 33,806 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 0.66 (33806 hom., cov: 32)
• Consequence: LINC02182 ENST00000563190.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0380
• Publications: 49 publications found

Genes affected

ZNF469 (HGNC:23216): (zinc finger protein 469) This gene encodes a zinc-finger protein. Low-percent homology to certain collagens suggests that it may function as a transcription factor or extra-nuclear regulator factor for the synthesis or organization of collagen fibers. Mutations in this gene cause brittle cornea syndrome. [provided by RefSeq, Jul 2008]

LINC02182 (HGNC:53044): (long intergenic non-protein coding RNA 2182)

ENSG00000300066 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.904 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000563190.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02182	ENST00000563190.1	TSL:3	n.344+3193C>A		intron	N/A
	LINC02182	ENST00000718466.1		n.364+3193C>A		intron	N/A
	LINC02182	ENST00000767800.1		n.246-4388C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.664 AC: 100844 AN: 151912 Hom.: 33753 Cov.: 32

Gnomad AFR AF: 0.677

Gnomad AMI AF: 0.526

Gnomad AMR AF: 0.750

Gnomad ASJ AF: 0.565

Gnomad EAS AF: 0.926

Gnomad SAS AF: 0.672

Gnomad FIN AF: 0.660

Gnomad MID AF: 0.627

Gnomad NFE AF: 0.623

Gnomad OTH AF: 0.673

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

GnomAD4 genome AF: 0.664 AC: 100953 AN: 152030 Hom.: 33806 Cov.: 32 AF XY: 0.667 AC XY: 49607 AN XY: 74318

African (AFR) AF: 0.677 AC: 28073 AN: 41444

American (AMR) AF: 0.751 AC: 11471 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.565 AC: 1957 AN: 3466

East Asian (EAS) AF: 0.926 AC: 4797 AN: 5180

South Asian (SAS) AF: 0.672 AC: 3241 AN: 4820

European-Finnish (FIN) AF: 0.660 AC: 6979 AN: 10574

Middle Eastern (MID) AF: 0.646 AC: 190 AN: 294

European-Non Finnish (NFE) AF: 0.623 AC: 42342 AN: 67958

Other (OTH) AF: 0.677 AC: 1425 AN: 2106

Alfa AF: 0.640 Hom.: 132887

Bravo AF: 0.674

Asia WGS AF: 0.786 AC: 2726 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.2
DANN	Benign	0.57
PhyloP100		0.038

Splicing

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

Other links and lift over

dbSNP: rs9938149; hg19: chr16-88331640;