rs6431734

Variant names:

• chr2-15734083-C-A
• rs6431734
• ENST00000436967.5:n.570-9406C>A

Your query was ambiguous. Multiple possible variants found:

• chr2-15734083-C-A
• chr2-15734083-C-G
• chr2-15734083-C-T

Variant summary

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

The ENST00000436967.5(LINC01804):​n.570-9406C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.697 in 152,000 control chromosomes in the GnomAD database, including 37,191 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 0.70 (37191 hom., cov: 32)
• Consequence: LINC01804 ENST00000436967.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.107
• Publications: 3 publications found

Genes affected

LINC01804 (HGNC:52596): (long intergenic non-protein coding RNA 1804)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.757 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000436967.5. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01804	ENST00000436967.5	TSL:3	n.570-9406C>A		intron	N/A
	LINC01804	ENST00000770646.1		n.528+32708C>A		intron	N/A
	LINC01804	ENST00000770647.1		n.406+32708C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.696 AC: 105780 AN: 151884 Hom.: 37150 Cov.: 32

Gnomad AFR AF: 0.717

Gnomad AMI AF: 0.692

Gnomad AMR AF: 0.769

Gnomad ASJ AF: 0.696

Gnomad EAS AF: 0.532

Gnomad SAS AF: 0.667

Gnomad FIN AF: 0.600

Gnomad MID AF: 0.744

Gnomad NFE AF: 0.696

Gnomad OTH AF: 0.728

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

GnomAD4 genome AF: 0.697 AC: 105875 AN: 152000 Hom.: 37191 Cov.: 32 AF XY: 0.693 AC XY: 51452 AN XY: 74280

African (AFR) AF: 0.717 AC: 29742 AN: 41458

American (AMR) AF: 0.769 AC: 11755 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.696 AC: 2416 AN: 3470

East Asian (EAS) AF: 0.532 AC: 2743 AN: 5160

South Asian (SAS) AF: 0.667 AC: 3206 AN: 4804

European-Finnish (FIN) AF: 0.600 AC: 6343 AN: 10566

Middle Eastern (MID) AF: 0.752 AC: 221 AN: 294

European-Non Finnish (NFE) AF: 0.696 AC: 47289 AN: 67940

Other (OTH) AF: 0.726 AC: 1532 AN: 2110

Alfa AF: 0.691 Hom.: 21047

Bravo AF: 0.710

Asia WGS AF: 0.635 AC: 2208 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	7.8
DANN	Benign	0.73
PhyloP100		-0.11

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: rs6431734;

hg19: chr2-15874207;