ENST00000563360.6:n.137-7192G>C

Variant names:

• chr16-79706644-G-C
• rs56738967
• ENST00000563360.6:n.137-7192G>C

Variant summary

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

The ENST00000563360.6(LINC01229):​n.137-7192G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.286 in 151,374 control chromosomes in the GnomAD database, including 6,458 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 0.29 (6458 hom., cov: 28)
• Consequence: LINC01229 ENST00000563360.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.514
• Publications: 15 publications found

Genes affected

LINC01229 (HGNC:49682): (long intergenic non-protein coding RNA 1229)

MAFTRR (HGNC:51525): (MAF transcriptional regulator RNA)

LOC105371356 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.314 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105371356	XR_001752268.2	n.375-7192G>C		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01229	ENST00000563360.6	n.137-7192G>C		intron_variant	Intron 1 of 3	4
LINC01229	ENST00000569164.2	n.159+30436G>C		intron_variant	Intron 1 of 3	4
LINC01229	ENST00000653222.1	n.150-7192G>C		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.286 AC: 43235 AN: 151256 Hom.: 6461 Cov.: 28

Gnomad AFR AF: 0.280

Gnomad AMI AF: 0.551

Gnomad AMR AF: 0.205

Gnomad ASJ AF: 0.248

Gnomad EAS AF: 0.268

Gnomad SAS AF: 0.117

Gnomad FIN AF: 0.298

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.317

Gnomad OTH AF: 0.282

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

GnomAD4 genome AF: 0.286 AC: 43240 AN: 151374 Hom.: 6458 Cov.: 28 AF XY: 0.278 AC XY: 20521 AN XY: 73924

African (AFR) AF: 0.280 AC: 11522 AN: 41214

American (AMR) AF: 0.204 AC: 3106 AN: 15194

Ashkenazi Jewish (ASJ) AF: 0.248 AC: 859 AN: 3464

East Asian (EAS) AF: 0.267 AC: 1365 AN: 5112

South Asian (SAS) AF: 0.116 AC: 556 AN: 4784

European-Finnish (FIN) AF: 0.298 AC: 3117 AN: 10450

Middle Eastern (MID) AF: 0.303 AC: 89 AN: 294

European-Non Finnish (NFE) AF: 0.317 AC: 21533 AN: 67856

Other (OTH) AF: 0.282 AC: 592 AN: 2096

Alfa AF: 0.298 Hom.: 826

Bravo AF: 0.283

Asia WGS AF: 0.178 AC: 618 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.59
DANN	Benign	0.39
PhyloP100		-0.51

Splicing

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

Other links and lift over

dbSNP: rs56738967; hg19: chr16-79740541;