rs6736997

Variant names:

• chr2-234706553-A-C
• rs6736997
• ENST00000629370.2:n.313+10805A>C

Your query was ambiguous. Multiple possible variants found:

• chr2-234706553-A-C
• chr2-234706553-A-T

Variant summary

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

The ENST00000629370.2(LINC01173):​n.313+10805A>C variant causes a intron 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 ENST00000629370.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.42
• Publications: 17 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000629370.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01173	NR_132376.1		n.201+10805A>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01173	ENST00000629370.2	TSL:3	n.313+10805A>C		intron	N/A
	LINC01173	ENST00000768858.1		n.222+10805A>C		intron	N/A
	LINC01173	ENST00000768859.1		n.199+10805A>C		intron	N/A

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

African (AFR) AF: 0.750 AC: 31121 AN: 41480

American (AMR) AF: 0.630 AC: 9622 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.663 AC: 2298 AN: 3468

East Asian (EAS) AF: 0.736 AC: 3805 AN: 5172

South Asian (SAS) AF: 0.518 AC: 2496 AN: 4814

European-Finnish (FIN) AF: 0.571 AC: 6025 AN: 10552

Middle Eastern (MID) AF: 0.718 AC: 211 AN: 294

European-Non Finnish (NFE) AF: 0.622 AC: 42320 AN: 67984

Other (OTH) AF: 0.675 AC: 1428 AN: 2114

Alfa AF: 0.638 Hom.: 87173

Bravo AF: 0.670

Asia WGS AF: 0.646 AC: 2250 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.50
DANN	Benign	0.51
PhyloP100		-2.4

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs6736997;

hg19: chr2-235615197;