rs17661170

Variant names:

• chr4-170254169-A-G
• rs17661170
• ENST00000654867.2:n.237-19490A>G

Your query was ambiguous. Multiple possible variants found:

• chr4-170254169-A-G
• chr4-170254169-A-T

Variant summary

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

The ENST00000654867.2(LINC01612):​n.237-19490A>G variant causes a intron 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 ENST00000654867.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0700
• Publications: 9 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LINC01612	NR_125889.1	n.194-22413A>G		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01612	ENST00000654867.2	n.237-19490A>G		intron_variant	Intron 1 of 3
LINC01612	ENST00000657650.1	n.197-22413A>G		intron_variant	Intron 1 of 3
LINC01612	ENST00000665566.3	n.244-22413A>G		intron_variant	Intron 1 of 3

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

African (AFR) AF: 0.159 AC: 6580 AN: 41500

American (AMR) AF: 0.275 AC: 4197 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.300 AC: 1038 AN: 3464

East Asian (EAS) AF: 0.652 AC: 3368 AN: 5162

South Asian (SAS) AF: 0.369 AC: 1774 AN: 4808

European-Finnish (FIN) AF: 0.368 AC: 3875 AN: 10536

Middle Eastern (MID) AF: 0.241 AC: 71 AN: 294

European-Non Finnish (NFE) AF: 0.258 AC: 17500 AN: 67956

Other (OTH) AF: 0.269 AC: 567 AN: 2110

Alfa AF: 0.253 Hom.: 8166

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
PhyloP100		0.070

Splicing

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

Other links and lift over

dbSNP: rs17661170; hg19: chr4-171175320;