rs17767491

Variant names:

• chr16-79711590-A-G
• rs17767491
• ENST00000563360.6:n.137-2246A>G

Variant summary

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

The ENST00000563360.6(LINC01229):​n.137-2246A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.248 in 151,986 control chromosomes in the GnomAD database, including 5,229 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 0.25 (5229 hom., cov: 32)
• Consequence: LINC01229 ENST00000563360.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.250
• Publications: 11 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=-0.92).
• 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.375-2246A>G		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01229	ENST00000563360.6	n.137-2246A>G		intron_variant	Intron 1 of 3	4
LINC01229	ENST00000569164.2	n.159+35382A>G		intron_variant	Intron 1 of 3	4
LINC01229	ENST00000653222.1	n.150-2246A>G		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.248 AC: 37662 AN: 151866 Hom.: 5236 Cov.: 32

Gnomad AFR AF: 0.148

Gnomad AMI AF: 0.549

Gnomad AMR AF: 0.190

Gnomad ASJ AF: 0.247

Gnomad EAS AF: 0.266

Gnomad SAS AF: 0.117

Gnomad FIN AF: 0.301

Gnomad MID AF: 0.292

Gnomad NFE AF: 0.318

Gnomad OTH AF: 0.253

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

GnomAD4 genome AF: 0.248 AC: 37646 AN: 151986 Hom.: 5229 Cov.: 32 AF XY: 0.242 AC XY: 17971 AN XY: 74280

African (AFR) AF: 0.148 AC: 6120 AN: 41474

American (AMR) AF: 0.189 AC: 2893 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.247 AC: 857 AN: 3468

East Asian (EAS) AF: 0.265 AC: 1368 AN: 5160

South Asian (SAS) AF: 0.116 AC: 558 AN: 4818

European-Finnish (FIN) AF: 0.301 AC: 3169 AN: 10544

Middle Eastern (MID) AF: 0.284 AC: 83 AN: 292

European-Non Finnish (NFE) AF: 0.317 AC: 21565 AN: 67932

Other (OTH) AF: 0.254 AC: 536 AN: 2108

Alfa AF: 0.278 Hom.: 1548

Bravo AF: 0.240

Asia WGS AF: 0.167 AC: 581 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.5
DANN	Benign	0.52
PhyloP100		-0.25

Splicing

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

Other links and lift over

dbSNP: rs17767491; hg19: chr16-79745487;