chr1-221882415-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 ENST00000715677.1(LINC01705):​n.634+36177C>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 ENST00000715677.1 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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000715677.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01705	ENST00000433576.6	TSL:5	n.572-1131C>G		intron	N/A
	LINC01705	ENST00000715677.1		n.634+36177C>G		intron	N/A
	LINC01705	ENST00000826165.1		n.476+36177C>G		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs12137702;

hg19: chr1-222055757;