chr3-28037594-C-T

Variant names:

• chr3-28037594-C-T
• rs170934
• ENST00000356047.4:n.28-8991G>A

Variant summary

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

The ENST00000356047.4(LINC01967):​n.28-8991G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.392 in 150,862 control chromosomes in the GnomAD database, including 12,666 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 (12666 hom., cov: 29)
• Consequence: LINC01967 ENST00000356047.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.14
• Publications: 29 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=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.473 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000356047.4. 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
	LINC01967	ENST00000356047.4	TSL:5	n.28-8991G>A		intron	N/A
	LINC01967	ENST00000437506.2	TSL:5	n.28-8991G>A		intron	N/A
	LINC01967	ENST00000746233.1		n.184+21648G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.392 AC: 59160 AN: 150744 Hom.: 12661 Cov.: 29

Gnomad AFR AF: 0.204

Gnomad AMI AF: 0.433

Gnomad AMR AF: 0.434

Gnomad ASJ AF: 0.510

Gnomad EAS AF: 0.450

Gnomad SAS AF: 0.393

Gnomad FIN AF: 0.438

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.477

Gnomad OTH AF: 0.443

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

GnomAD4 genome AF: 0.392 AC: 59172 AN: 150862 Hom.: 12666 Cov.: 29 AF XY: 0.391 AC XY: 28756 AN XY: 73568

African (AFR) AF: 0.204 AC: 8366 AN: 41008

American (AMR) AF: 0.434 AC: 6581 AN: 15180

Ashkenazi Jewish (ASJ) AF: 0.510 AC: 1763 AN: 3456

East Asian (EAS) AF: 0.450 AC: 2297 AN: 5100

South Asian (SAS) AF: 0.394 AC: 1876 AN: 4766

European-Finnish (FIN) AF: 0.438 AC: 4496 AN: 10274

Middle Eastern (MID) AF: 0.483 AC: 142 AN: 294

European-Non Finnish (NFE) AF: 0.477 AC: 32337 AN: 67782

Other (OTH) AF: 0.440 AC: 922 AN: 2096

Alfa AF: 0.450 Hom.: 62522

Bravo AF: 0.382

Asia WGS AF: 0.392 AC: 1363 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.089
DANN	Benign	0.24
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs170934; hg19: chr3-28079085;