rs17661170

chr4-170254169-A-Gchr4-170254169-A-T

Variant summary

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

The NR_125889.1(LINC01612):n.194-22413A>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 0.257 in 152,006 control chromosomes in the GnomAD database, including 5,758 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 0.26 (5758 hom., cov: 31)
• Consequence: LINC01612 NR_125889.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0700

Genes affected

LINC01612 (HGNC:51837): (long intergenic non-protein coding RNA 1612)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.634 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01612	NR_125889.1	n.194-22413A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01612	ENST00000667527.2	n.250-22413A>G		intron_variant, non_coding_transcript_variant
LINC01612	ENST00000654867.1	n.197-19490A>G		intron_variant, non_coding_transcript_variant
LINC01612	ENST00000657650.1	n.197-22413A>G		intron_variant, non_coding_transcript_variant
LINC01612	ENST00000665566.2	n.244-22413A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.257 AC: 39070 AN: 151888 Hom.: 5757 Cov.: 31

Gnomad AFR AF: 0.159

Gnomad AMI AF: 0.127

Gnomad AMR AF: 0.275

Gnomad ASJ AF: 0.300

Gnomad EAS AF: 0.653

Gnomad SAS AF: 0.369

Gnomad FIN AF: 0.368

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.258

Gnomad OTH AF: 0.263

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

GnomAD4 genome AF: 0.257 AC: 39086 AN: 152006 Hom.: 5758 Cov.: 31 AF XY: 0.268 AC XY: 19870 AN XY: 74278

Gnomad4 AFR AF: 0.159

Gnomad4 AMR AF: 0.275

Gnomad4 ASJ AF: 0.300

Gnomad4 EAS AF: 0.652

Gnomad4 SAS AF: 0.369

Gnomad4 FIN AF: 0.368

Gnomad4 NFE AF: 0.258

Gnomad4 OTH AF: 0.269

Alfa AF: 0.254 Hom.: 6969

Bravo AF: 0.248

Asia WGS AF: 0.480 AC: 1668 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	4.6
Dann	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17661170; hg19: chr4-171175320;