1-84631237-A-G

Variant names:

• chr1-84631237-A-G
• rs6695249
• ENST00000370624.1:n.227-350T>C

Variant summary

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

The ENST00000370624.1(LINC01555):​n.227-350T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.182 in 367,004 control chromosomes in the GnomAD database, including 6,801 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 (2851 hom., cov: 32)
  • Exomes 𝑓: 0.18 (3950 hom.)
• Consequence: LINC01555 ENST00000370624.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0310
• Publications: 3 publications found

Genes affected

LINC01555 (HGNC:26647): (long intergenic non-protein coding RNA 1555)

LOC124904206 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.241 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000370624.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01555	NR_027379.1		n.227-350T>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01555	ENST00000370624.1	TSL:2	n.227-350T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.187 AC: 28411 AN: 152076 Hom.: 2834 Cov.: 32

Gnomad AFR AF: 0.244

Gnomad AMI AF: 0.329

Gnomad AMR AF: 0.228

Gnomad ASJ AF: 0.219

Gnomad EAS AF: 0.0593

Gnomad SAS AF: 0.227

Gnomad FIN AF: 0.121

Gnomad MID AF: 0.276

Gnomad NFE AF: 0.156

Gnomad OTH AF: 0.197

GnomAD4 exome AF: 0.178 AC: 38251 AN: 214806 Hom.: 3950 AF XY: 0.185 AC XY: 22188 AN XY: 120238

African (AFR) AF: 0.246 AC: 1367 AN: 5566

American (AMR) AF: 0.257 AC: 3167 AN: 12346

Ashkenazi Jewish (ASJ) AF: 0.217 AC: 1358 AN: 6254

East Asian (EAS) AF: 0.0559 AC: 470 AN: 8410

South Asian (SAS) AF: 0.237 AC: 10138 AN: 42818

European-Finnish (FIN) AF: 0.129 AC: 1190 AN: 9252

Middle Eastern (MID) AF: 0.292 AC: 697 AN: 2384

European-Non Finnish (NFE) AF: 0.154 AC: 18069 AN: 117482

Other (OTH) AF: 0.174 AC: 1795 AN: 10294

GnomAD4 genome AF: 0.187 AC: 28475 AN: 152198 Hom.: 2851 Cov.: 32 AF XY: 0.187 AC XY: 13887 AN XY: 74426

African (AFR) AF: 0.245 AC: 10153 AN: 41472

American (AMR) AF: 0.228 AC: 3478 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.219 AC: 759 AN: 3472

East Asian (EAS) AF: 0.0594 AC: 308 AN: 5184

South Asian (SAS) AF: 0.228 AC: 1101 AN: 4822

European-Finnish (FIN) AF: 0.121 AC: 1285 AN: 10612

Middle Eastern (MID) AF: 0.282 AC: 83 AN: 294

European-Non Finnish (NFE) AF: 0.156 AC: 10596 AN: 68034

Other (OTH) AF: 0.195 AC: 412 AN: 2116

Alfa AF: 0.172 Hom.: 3627

Bravo AF: 0.196

Asia WGS AF: 0.146 AC: 508 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.4
DANN	Benign	0.76
PhyloP100		-0.031
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs6695249; hg19: chr1-85096920; COSMIC: COSV59226043;