rs1399685

chr2-146870842-T-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000696349.1(LINC01911):n.727-7080T>A 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 0.0311 in 152,222 control chromosomes in the GnomAD database, including 106 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 0.031 (106 hom., cov: 32)
• Consequence: LINC01911 ENST00000696349.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.117

Genes affected

LINC01911 (HGNC:52730): (long intergenic non-protein coding RNA 1911)

LOC105373668 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0311 (4736/152222) while in subpopulation NFE AF= 0.0498 (3389/68002). AF 95% confidence interval is 0.0484. There are 106 homozygotes in gnomad4. There are 2206 alleles in male gnomad4 subpopulation. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd at 106 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105373668	XR_923426.3	n.2178+3195T>A		intron_variant, non_coding_transcript_variant
LOC105373668	XR_007087256.1	n.713+3195T>A		intron_variant, non_coding_transcript_variant
LOC105373668	XR_007087257.1	n.2178+3195T>A		intron_variant, non_coding_transcript_variant
LOC105373668	XR_923428.3	n.2151+3195T>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01911	ENST00000696349.1	n.727-7080T>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0311 AC: 4738 AN: 152104 Hom.: 106 Cov.: 32

Gnomad AFR AF: 0.00896

Gnomad AMI AF: 0.0110

Gnomad AMR AF: 0.0306

Gnomad ASJ AF: 0.0158

Gnomad EAS AF: 0.000577

Gnomad SAS AF: 0.00787

Gnomad FIN AF: 0.0291

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0498

Gnomad OTH AF: 0.0401

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

GnomAD4 genome AF: 0.0311 AC: 4736 AN: 152222 Hom.: 106 Cov.: 32 AF XY: 0.0296 AC XY: 2206 AN XY: 74418

Gnomad4 AFR AF: 0.00893

Gnomad4 AMR AF: 0.0305

Gnomad4 ASJ AF: 0.0158

Gnomad4 EAS AF: 0.000579

Gnomad4 SAS AF: 0.00767

Gnomad4 FIN AF: 0.0291

Gnomad4 NFE AF: 0.0498

Gnomad4 OTH AF: 0.0397

Alfa AF: 0.0389 Hom.: 13

Bravo AF: 0.0313

Asia WGS AF: 0.00577 AC: 20 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	6.7
Dann	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1399685; hg19: chr2-147628410;