rs6431734

Variant names:

• chr2-15734083-C-A
• rs6431734
• ENST00000436967.4:n.283-9406C>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. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000436967.4(LINC01804):​n.283-9406C>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 ENST00000436967.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.107

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01804	ENST00000436967.4	n.283-9406C>A		intron_variant	Intron 2 of 3	3

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

Gnomad4 AFR AF: 0.717

Gnomad4 AMR AF: 0.769

Gnomad4 ASJ AF: 0.696

Gnomad4 EAS AF: 0.532

Gnomad4 SAS AF: 0.667

Gnomad4 FIN AF: 0.600

Gnomad4 NFE AF: 0.696

Gnomad4 OTH AF: 0.726

Alfa AF: 0.691 Hom.: 19010

Bravo AF: 0.710

Asia WGS AF: 0.635 AC: 2208 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6431734; hg19: chr2-15874207;