rs6736997

Positions:

• chr2-234706553-A-C

Variant summary

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

The NR_132376.1(LINC01173):​n.201+10805A>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 0.656 in 152,072 control chromosomes in the GnomAD database, including 33,104 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 0.66 (33104 hom., cov: 32)
• Consequence: LINC01173 NR_132376.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.42

Genes affected

LINC01173 (HGNC:49545): (long intergenic non-protein coding RNA 1173)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.743 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC01173	NR_132376.1	n.201+10805A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01173	ENST00000629370.1	n.201+10805A>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.656 AC: 99676 AN: 151954 Hom.: 33060 Cov.: 32

Gnomad AFR AF: 0.750

Gnomad AMI AF: 0.500

Gnomad AMR AF: 0.629

Gnomad ASJ AF: 0.663

Gnomad EAS AF: 0.736

Gnomad SAS AF: 0.518

Gnomad FIN AF: 0.571

Gnomad MID AF: 0.706

Gnomad NFE AF: 0.622

Gnomad OTH AF: 0.672

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

GnomAD4 genome AF: 0.656 AC: 99781 AN: 152072 Hom.: 33104 Cov.: 32 AF XY: 0.652 AC XY: 48479 AN XY: 74328

Gnomad4 AFR AF: 0.750

Gnomad4 AMR AF: 0.630

Gnomad4 ASJ AF: 0.663

Gnomad4 EAS AF: 0.736

Gnomad4 SAS AF: 0.518

Gnomad4 FIN AF: 0.571

Gnomad4 NFE AF: 0.622

Gnomad4 OTH AF: 0.675

Alfa AF: 0.631 Hom.: 35067

Bravo AF: 0.670

Asia WGS AF: 0.646 AC: 2250 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.50
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6736997; hg19: chr2-235615197;