16-79710504-G-A

Variant names:

• chr16-79710504-G-A
• rs17767383
• ENST00000563360.6:n.137-3332G>A

Variant summary

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

The ENST00000563360.6(LINC01229):​n.137-3332G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.278 in 152,072 control chromosomes in the GnomAD database, including 6,146 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 0.28 (6146 hom., cov: 32)
• Consequence: LINC01229 ENST00000563360.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.58
• Publications: 8 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=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.313 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000563360.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01229	ENST00000563360.6	TSL:4	n.137-3332G>A		intron	N/A
	LINC01229	ENST00000569164.2	TSL:4	n.159+34296G>A		intron	N/A
	LINC01229	ENST00000653222.1		n.150-3332G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.279 AC: 42337 AN: 151954 Hom.: 6153 Cov.: 32

Gnomad AFR AF: 0.255

Gnomad AMI AF: 0.547

Gnomad AMR AF: 0.204

Gnomad ASJ AF: 0.247

Gnomad EAS AF: 0.267

Gnomad SAS AF: 0.118

Gnomad FIN AF: 0.300

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.317

Gnomad OTH AF: 0.277

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

GnomAD4 genome AF: 0.278 AC: 42330 AN: 152072 Hom.: 6146 Cov.: 32 AF XY: 0.271 AC XY: 20146 AN XY: 74322

African (AFR) AF: 0.255 AC: 10572 AN: 41492

American (AMR) AF: 0.203 AC: 3106 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.247 AC: 857 AN: 3470

East Asian (EAS) AF: 0.266 AC: 1379 AN: 5178

South Asian (SAS) AF: 0.117 AC: 563 AN: 4820

European-Finnish (FIN) AF: 0.300 AC: 3164 AN: 10554

Middle Eastern (MID) AF: 0.299 AC: 88 AN: 294

European-Non Finnish (NFE) AF: 0.317 AC: 21520 AN: 67976

Other (OTH) AF: 0.276 AC: 582 AN: 2106

Alfa AF: 0.305 Hom.: 30586

Bravo AF: 0.275

Asia WGS AF: 0.171 AC: 596 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.12
DANN	Benign	0.51
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs17767383; hg19: chr16-79744401;