rs4650135

Positions:

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

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_183659.1(LINC02791):​n.357-3308A>G variant causes a intron, non coding transcript 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 NR_183659.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.60

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

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
LINC02791	NR_183659.1	n.357-3308A>G		intron_variant, non_coding_transcript_variant
LOC105378787	XR_947486.2	n.891+881T>C		intron_variant, non_coding_transcript_variant
LINC02791	NR_183660.1	n.429-3308A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02791	ENST00000650525.1	n.264-1064A>G		intron_variant, non_coding_transcript_variant
LINC01707	ENST00000658427.1	n.399+881T>C		intron_variant, non_coding_transcript_variant
LINC01707	ENST00000667473.1	n.803+881T>C		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.345

Gnomad4 AMR AF: 0.161

Gnomad4 ASJ AF: 0.110

Gnomad4 EAS AF: 0.327

Gnomad4 SAS AF: 0.250

Gnomad4 FIN AF: 0.241

Gnomad4 NFE AF: 0.150

Gnomad4 OTH AF: 0.186

Alfa AF: 0.160 Hom.: 4008

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4650135; hg19: chr1-69684997;