rs669607

Positions:

• chr3-28029953-A-C
• chr3-28029953-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000356047.4(LINC01967):​n.28-1350T>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.38 in 151,804 control chromosomes in the GnomAD database, including 12,439 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 0.38 (12439 hom., cov: 31)
• Consequence: LINC01967 ENST00000356047.4 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.120

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01967	ENST00000356047.4	n.28-1350T>G		intron_variant, non_coding_transcript_variant		5
LINC01967	ENST00000437506.2	n.28-1350T>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.380 AC: 57703 AN: 151686 Hom.: 12434 Cov.: 31

Gnomad AFR AF: 0.161

Gnomad AMI AF: 0.432

Gnomad AMR AF: 0.430

Gnomad ASJ AF: 0.508

Gnomad EAS AF: 0.460

Gnomad SAS AF: 0.403

Gnomad FIN AF: 0.433

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.477

Gnomad OTH AF: 0.435

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

GnomAD4 genome AF: 0.380 AC: 57713 AN: 151804 Hom.: 12439 Cov.: 31 AF XY: 0.379 AC XY: 28148 AN XY: 74178

Gnomad4 AFR AF: 0.161

Gnomad4 AMR AF: 0.430

Gnomad4 ASJ AF: 0.508

Gnomad4 EAS AF: 0.461

Gnomad4 SAS AF: 0.403

Gnomad4 FIN AF: 0.433

Gnomad4 NFE AF: 0.477

Gnomad4 OTH AF: 0.432

Alfa AF: 0.468 Hom.: 36531

Bravo AF: 0.369

Asia WGS AF: 0.396 AC: 1376 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.1
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs669607; hg19: chr3-28071444;