rs12666691

Variant names:

• chr7-134432202-C-G
• rs12666691
• ENST00000607945.2:n.118+112G>C

Variant summary

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

The ENST00000607945.2(LINC03060):​n.118+112G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.191 in 153,204 control chromosomes in the GnomAD database, including 2,883 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 0.19 (2863 hom., cov: 33)
  • Exomes 𝑓: 0.17 (20 hom.)
• Consequence: LINC03060 ENST00000607945.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.274
• Publications: 1 publications found

Genes affected

LINC03060 (HGNC:56367): (long intergenic non-protein coding RNA 3060)

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 = 0.288 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC03060	NR_183388.1	n.107+112G>C		intron_variant	Intron 1 of 1
LINC03060	NR_183389.1	n.107+112G>C		intron_variant	Intron 1 of 4
LINC03060	NR_183390.1	n.107+112G>C		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC03060	ENST00000607945.2	n.118+112G>C		intron_variant	Intron 1 of 2	4
LINC03060	ENST00000609209.2	n.123+112G>C		intron_variant	Intron 1 of 2	5
LINC03060	ENST00000609619.3	n.187+112G>C		intron_variant	Intron 1 of 1	2

Frequencies

GnomAD3 genomes AF: 0.191 AC: 29032 AN: 152044 Hom.: 2858 Cov.: 33

Gnomad AFR AF: 0.233

Gnomad AMI AF: 0.0603

Gnomad AMR AF: 0.141

Gnomad ASJ AF: 0.0953

Gnomad EAS AF: 0.301

Gnomad SAS AF: 0.126

Gnomad FIN AF: 0.190

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.180

Gnomad OTH AF: 0.182

GnomAD4 exome AF: 0.174 AC: 181 AN: 1042 Hom.: 20 AF XY: 0.167 AC XY: 116 AN XY: 696

African (AFR) AF: 0.125 AC: 4 AN: 32

American (AMR) AF: 0.136 AC: 12 AN: 88

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 32

East Asian (EAS) AF: 0.323 AC: 31 AN: 96

South Asian (SAS) AF: 0.125 AC: 14 AN: 112

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 4

Middle Eastern (MID) AF: 0.125 AC: 1 AN: 8

European-Non Finnish (NFE) AF: 0.179 AC: 112 AN: 626

Other (OTH) AF: 0.159 AC: 7 AN: 44

GnomAD4 genome AF: 0.191 AC: 29052 AN: 152162 Hom.: 2863 Cov.: 33 AF XY: 0.189 AC XY: 14066 AN XY: 74372

African (AFR) AF: 0.232 AC: 9634 AN: 41490

American (AMR) AF: 0.141 AC: 2154 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0953 AC: 331 AN: 3472

East Asian (EAS) AF: 0.301 AC: 1555 AN: 5170

South Asian (SAS) AF: 0.126 AC: 606 AN: 4820

European-Finnish (FIN) AF: 0.190 AC: 2012 AN: 10580

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.180 AC: 12269 AN: 68012

Other (OTH) AF: 0.184 AC: 389 AN: 2112

Alfa AF: 0.184 Hom.: 313

Bravo AF: 0.190

Asia WGS AF: 0.234 AC: 815 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	5.1
DANN	Benign	0.45
PhyloP100		-0.27
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs12666691; hg19: chr7-134116954;