rs7188445

Variant names:

• chr16-79701090-G-A
• rs7188445
• ENST00000563360.6:n.137-12746G>A

Your query was ambiguous. Multiple possible variants found:

• chr16-79701090-G-A
• chr16-79701090-G-T

Variant summary

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

The ENST00000563360.6(LINC01229):​n.137-12746G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.288 in 151,728 control chromosomes in the GnomAD database, including 6,549 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 (6549 hom., cov: 31)
• Consequence: LINC01229 ENST00000563360.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.252
• Publications: 42 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=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.326 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105371356	XR_001752268.2	n.375-12746G>A		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01229	ENST00000563360.6	n.137-12746G>A		intron_variant	Intron 1 of 3	4
LINC01229	ENST00000569164.2	n.159+24882G>A		intron_variant	Intron 1 of 3	4
LINC01229	ENST00000653222.1	n.150-12746G>A		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.288 AC: 43636 AN: 151610 Hom.: 6554 Cov.: 31

Gnomad AFR AF: 0.261

Gnomad AMI AF: 0.550

Gnomad AMR AF: 0.209

Gnomad ASJ AF: 0.254

Gnomad EAS AF: 0.289

Gnomad SAS AF: 0.129

Gnomad FIN AF: 0.300

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.329

Gnomad OTH AF: 0.282

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

GnomAD4 genome AF: 0.288 AC: 43635 AN: 151728 Hom.: 6549 Cov.: 31 AF XY: 0.280 AC XY: 20747 AN XY: 74120

African (AFR) AF: 0.261 AC: 10789 AN: 41348

American (AMR) AF: 0.208 AC: 3183 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.254 AC: 880 AN: 3466

East Asian (EAS) AF: 0.288 AC: 1479 AN: 5134

South Asian (SAS) AF: 0.129 AC: 620 AN: 4820

European-Finnish (FIN) AF: 0.300 AC: 3151 AN: 10486

Middle Eastern (MID) AF: 0.320 AC: 94 AN: 294

European-Non Finnish (NFE) AF: 0.329 AC: 22343 AN: 67888

Other (OTH) AF: 0.282 AC: 594 AN: 2106

Alfa AF: 0.297 Hom.: 2012

Bravo AF: 0.284

Asia WGS AF: 0.188 AC: 653 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	3.7
DANN	Benign	0.83
PhyloP100		0.25

Splicing

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

Other links and lift over

dbSNP: rs7188445; hg19: chr16-79734987;