rs4650135

Variant names:

• chr1-69219314-T-C
• rs4650135
• ENST00000650525.1:n.264-1064A>G

Your query was ambiguous. Multiple possible variants found:

• chr1-69219314-T-C
• chr1-69219314-T-G

Variant summary

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

The ENST00000650525.1(LINC02791):​n.264-1064A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.219 in 152,090 control chromosomes in the GnomAD database, including 4,209 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 0.22 (4209 hom., cov: 32)
• Consequence: LINC02791 ENST00000650525.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.60
• Publications: 10 publications found

Genes affected

LINC02791 (HGNC:54315): (long intergenic non-protein coding RNA 2791)

LINC01707 (HGNC:52495): (long intergenic non-protein coding RNA 1707)

LOC105378787 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.34 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02791	NR_183659.1	n.357-3308A>G		intron_variant	Intron 2 of 2
LINC02791	NR_183660.1	n.429-3308A>G		intron_variant	Intron 3 of 3
LOC105378787	XR_947486.2	n.891+881T>C		intron_variant	Intron 6 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02791	ENST00000650525.1	n.264-1064A>G		intron_variant	Intron 1 of 3
LINC01707	ENST00000658427.1	n.399+881T>C		intron_variant	Intron 3 of 3
LINC01707	ENST00000667473.1	n.803+881T>C		intron_variant	Intron 6 of 6

Frequencies

GnomAD3 genomes AF: 0.219 AC: 33262 AN: 151970 Hom.: 4199 Cov.: 32

Gnomad AFR AF: 0.345

Gnomad AMI AF: 0.110

Gnomad AMR AF: 0.161

Gnomad ASJ AF: 0.110

Gnomad EAS AF: 0.326

Gnomad SAS AF: 0.250

Gnomad FIN AF: 0.241

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.150

Gnomad OTH AF: 0.185

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

GnomAD4 genome AF: 0.219 AC: 33312 AN: 152090 Hom.: 4209 Cov.: 32 AF XY: 0.223 AC XY: 16592 AN XY: 74330

African (AFR) AF: 0.345 AC: 14307 AN: 41478

American (AMR) AF: 0.161 AC: 2465 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.110 AC: 383 AN: 3472

East Asian (EAS) AF: 0.327 AC: 1682 AN: 5150

South Asian (SAS) AF: 0.250 AC: 1203 AN: 4820

European-Finnish (FIN) AF: 0.241 AC: 2548 AN: 10580

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.150 AC: 10193 AN: 67992

Other (OTH) AF: 0.186 AC: 393 AN: 2108

Alfa AF: 0.175 Hom.: 7226

Bravo AF: 0.222

Asia WGS AF: 0.294 AC: 1023 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.12
DANN	Benign	0.54
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs4650135; hg19: chr1-69684997;