chr16-79813376-C-T

Variant names:

• chr16-79813376-C-T
• rs11150219
• ENST00000567966.2:n.198+13612G>A

Variant summary

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

The ENST00000567966.2(LINC01228):​n.198+13612G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.6 in 152,030 control chromosomes in the GnomAD database, including 33,052 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 0.60 (33052 hom., cov: 31)
• Consequence: LINC01228 ENST00000567966.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.173
• Publications: 1 publications found

Genes affected

LINC01228 (HGNC:49681): (long intergenic non-protein coding RNA 1228)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.777 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000567966.2. 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
	LINC01228	NR_170199.1		n.163+13612G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01228	ENST00000567966.2	TSL:3	n.198+13612G>A		intron	N/A
	LINC01228	ENST00000766963.1		n.182-13089G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.600 AC: 91187 AN: 151912 Hom.: 33061 Cov.: 31

Gnomad AFR AF: 0.163

Gnomad AMI AF: 0.939

Gnomad AMR AF: 0.726

Gnomad ASJ AF: 0.766

Gnomad EAS AF: 0.699

Gnomad SAS AF: 0.682

Gnomad FIN AF: 0.780

Gnomad MID AF: 0.585

Gnomad NFE AF: 0.783

Gnomad OTH AF: 0.626

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

GnomAD4 genome AF: 0.600 AC: 91168 AN: 152030 Hom.: 33052 Cov.: 31 AF XY: 0.602 AC XY: 44743 AN XY: 74282

African (AFR) AF: 0.163 AC: 6761 AN: 41484

American (AMR) AF: 0.727 AC: 11086 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.766 AC: 2656 AN: 3468

East Asian (EAS) AF: 0.699 AC: 3602 AN: 5156

South Asian (SAS) AF: 0.682 AC: 3285 AN: 4816

European-Finnish (FIN) AF: 0.780 AC: 8231 AN: 10552

Middle Eastern (MID) AF: 0.588 AC: 173 AN: 294

European-Non Finnish (NFE) AF: 0.783 AC: 53210 AN: 67974

Other (OTH) AF: 0.618 AC: 1308 AN: 2116

Alfa AF: 0.718 Hom.: 103103

Bravo AF: 0.582

Asia WGS AF: 0.609 AC: 2120 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.0
DANN	Benign	0.45
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs11150219; hg19: chr16-79847273;