chr1-188908556-A-C

Position:

• chr1-188908556-A-C

Variant summary

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

The NR_174955.1(LINC01035):​n.255+2630A>C 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 0.0956 in 152,036 control chromosomes in the GnomAD database, including 1,963 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 0.096 (1963 hom., cov: 32)
• Consequence: LINC01035 NR_174955.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.269

Genes affected

LINC01035 (HGNC:49022): (long intergenic non-protein coding RNA 1035)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.298 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01035	NR_174955.1	n.255+2630A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01035	ENST00000658142.1	n.157+2630A>C		intron_variant, non_coding_transcript_variant
LINC01035	ENST00000445072.1	n.239+2630A>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.0952 AC: 14464 AN: 151920 Hom.: 1956 Cov.: 32

Gnomad AFR AF: 0.302

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0388

Gnomad ASJ AF: 0.0395

Gnomad EAS AF: 0.0574

Gnomad SAS AF: 0.0553

Gnomad FIN AF: 0.00235

Gnomad MID AF: 0.0160

Gnomad NFE AF: 0.00727

Gnomad OTH AF: 0.0776

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

GnomAD4 genome AF: 0.0956 AC: 14528 AN: 152036 Hom.: 1963 Cov.: 32 AF XY: 0.0925 AC XY: 6877 AN XY: 74320

Gnomad4 AFR AF: 0.303

Gnomad4 AMR AF: 0.0387

Gnomad4 ASJ AF: 0.0395

Gnomad4 EAS AF: 0.0573

Gnomad4 SAS AF: 0.0553

Gnomad4 FIN AF: 0.00235

Gnomad4 NFE AF: 0.00727

Gnomad4 OTH AF: 0.0791

Alfa AF: 0.00397 Hom.: 3

Bravo AF: 0.107

Asia WGS AF: 0.0980 AC: 340 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	3.3
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10494619; hg19: chr1-188877687;