3-27979061-T-C

Variant names:

• chr3-27979061-T-C
• rs12632457
• ENST00000643609.1:n.135+8309A>G

Variant summary

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

The ENST00000643609.1(LINC01967):​n.135+8309A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.387 in 151,706 control chromosomes in the GnomAD database, including 11,499 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 0.39 (11499 hom., cov: 31)
• Consequence: LINC01967 ENST00000643609.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0870
• Publications: 4 publications found

Genes affected

LINC01967 (HGNC:52793): (long intergenic non-protein coding RNA 1967)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.464 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01967	ENST00000643609.1	n.135+8309A>G		intron_variant	Intron 2 of 6
LINC01967	ENST00000746233.1	n.379-26216A>G		intron_variant	Intron 4 of 7

Frequencies

GnomAD3 genomes AF: 0.387 AC: 58605 AN: 151590 Hom.: 11499 Cov.: 31

Gnomad AFR AF: 0.410

Gnomad AMI AF: 0.383

Gnomad AMR AF: 0.303

Gnomad ASJ AF: 0.347

Gnomad EAS AF: 0.479

Gnomad SAS AF: 0.480

Gnomad FIN AF: 0.428

Gnomad MID AF: 0.296

Gnomad NFE AF: 0.374

Gnomad OTH AF: 0.365

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

GnomAD4 genome AF: 0.387 AC: 58636 AN: 151706 Hom.: 11499 Cov.: 31 AF XY: 0.388 AC XY: 28764 AN XY: 74132

African (AFR) AF: 0.410 AC: 16966 AN: 41396

American (AMR) AF: 0.303 AC: 4607 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.347 AC: 1204 AN: 3466

East Asian (EAS) AF: 0.478 AC: 2466 AN: 5154

South Asian (SAS) AF: 0.480 AC: 2308 AN: 4808

European-Finnish (FIN) AF: 0.428 AC: 4512 AN: 10540

Middle Eastern (MID) AF: 0.281 AC: 82 AN: 292

European-Non Finnish (NFE) AF: 0.374 AC: 25374 AN: 67812

Other (OTH) AF: 0.365 AC: 769 AN: 2104

Alfa AF: 0.373 Hom.: 44702

Bravo AF: 0.375

Asia WGS AF: 0.492 AC: 1709 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.5
DANN	Benign	0.85
PhyloP100		0.087

Splicing

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

Other links and lift over

dbSNP: rs12632457; hg19: chr3-28020552;