1-221882415-G-C

Variant names:

• chr1-221882415-G-C
• rs12137702
• ENST00000433576.6:n.572-1131C>G

Variant summary

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

The ENST00000433576.6(LINC01705):​n.572-1131C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.266 in 151,940 control chromosomes in the GnomAD database, including 6,018 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 0.27 (6018 hom., cov: 31)
• Consequence: LINC01705 ENST00000433576.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.194
• Publications: 2 publications found

Genes affected

LINC01705 (HGNC:52493): (long intergenic non-protein coding RNA 1705)

ENSG00000307440 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.322 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124904517	XR_007066885.1	n.330+30350G>C		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01705	ENST00000433576.6	n.572-1131C>G		intron_variant	Intron 5 of 5	5
LINC01705	ENST00000715677.1	n.634+36177C>G		intron_variant	Intron 4 of 4
LINC01705	ENST00000826165.1	n.476+36177C>G		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.266 AC: 40445 AN: 151822 Hom.: 6017 Cov.: 31

Gnomad AFR AF: 0.193

Gnomad AMI AF: 0.364

Gnomad AMR AF: 0.213

Gnomad ASJ AF: 0.322

Gnomad EAS AF: 0.00193

Gnomad SAS AF: 0.250

Gnomad FIN AF: 0.358

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.325

Gnomad OTH AF: 0.291

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

GnomAD4 genome AF: 0.266 AC: 40440 AN: 151940 Hom.: 6018 Cov.: 31 AF XY: 0.264 AC XY: 19584 AN XY: 74244

African (AFR) AF: 0.192 AC: 7970 AN: 41430

American (AMR) AF: 0.212 AC: 3242 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.322 AC: 1115 AN: 3466

East Asian (EAS) AF: 0.00193 AC: 10 AN: 5170

South Asian (SAS) AF: 0.250 AC: 1200 AN: 4806

European-Finnish (FIN) AF: 0.358 AC: 3768 AN: 10538

Middle Eastern (MID) AF: 0.299 AC: 88 AN: 294

European-Non Finnish (NFE) AF: 0.325 AC: 22114 AN: 67956

Other (OTH) AF: 0.286 AC: 602 AN: 2108

Alfa AF: 0.171 Hom.: 372

Bravo AF: 0.250

Asia WGS AF: 0.100 AC: 351 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	0.51
DANN	Benign	0.82
PhyloP100		-0.19

Splicing

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

Other links and lift over

dbSNP: rs12137702; hg19: chr1-222055757;