chr1-100611655-T-C

Variant names:

• chr1-100611655-T-C
• rs2027166
• ENST00000773974.1:n.164+8888A>G

Variant summary

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

The ENST00000773974.1(LINC01349):​n.164+8888A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.209 in 152,014 control chromosomes in the GnomAD database, including 3,447 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 0.21 (3447 hom., cov: 32)
• Consequence: LINC01349 ENST00000773974.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.24
• Publications: 3 publications found

Genes affected

LINC01349 (HGNC:50568): (long intergenic non-protein coding RNA 1349)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.52).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.235 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01349	ENST00000773974.1	n.164+8888A>G		intron_variant	Intron 3 of 3
LINC01349	ENST00000773975.1	n.124+33515A>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.209 AC: 31715 AN: 151896 Hom.: 3440 Cov.: 32

Gnomad AFR AF: 0.239

Gnomad AMI AF: 0.251

Gnomad AMR AF: 0.202

Gnomad ASJ AF: 0.249

Gnomad EAS AF: 0.144

Gnomad SAS AF: 0.189

Gnomad FIN AF: 0.261

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.187

Gnomad OTH AF: 0.242

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

GnomAD4 genome AF: 0.209 AC: 31741 AN: 152014 Hom.: 3447 Cov.: 32 AF XY: 0.210 AC XY: 15633 AN XY: 74286

African (AFR) AF: 0.239 AC: 9899 AN: 41476

American (AMR) AF: 0.202 AC: 3078 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.249 AC: 864 AN: 3470

East Asian (EAS) AF: 0.144 AC: 744 AN: 5184

South Asian (SAS) AF: 0.189 AC: 909 AN: 4804

European-Finnish (FIN) AF: 0.261 AC: 2750 AN: 10518

Middle Eastern (MID) AF: 0.211 AC: 62 AN: 294

European-Non Finnish (NFE) AF: 0.187 AC: 12698 AN: 67982

Other (OTH) AF: 0.241 AC: 509 AN: 2112

Alfa AF: 0.194 Hom.: 449

Bravo AF: 0.207

Asia WGS AF: 0.180 AC: 628 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.52
CADD	Benign	20
DANN	Benign	0.78
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs2027166; hg19: chr1-101077211;