rs6431731

Variant names:

• chr2-15722878-C-T
• rs6431731
• ENST00000436967.5:n.570-20611C>T

Variant summary

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

The ENST00000436967.5(LINC01804):​n.570-20611C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.969 in 152,220 control chromosomes in the GnomAD database, including 71,519 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 0.97 (71519 hom., cov: 30)
• Consequence: LINC01804 ENST00000436967.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.66
• Publications: 14 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=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.982 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	ENST00000436967.5	n.570-20611C>T		intron_variant	Intron 3 of 4	3
LINC01804	ENST00000770646.1	n.528+21503C>T		intron_variant	Intron 3 of 4
LINC01804	ENST00000770647.1	n.406+21503C>T		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.969 AC: 147412 AN: 152102 Hom.: 71458 Cov.: 30

Gnomad AFR AF: 0.990

Gnomad AMI AF: 0.989

Gnomad AMR AF: 0.980

Gnomad ASJ AF: 0.985

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.992

Gnomad FIN AF: 0.972

Gnomad MID AF: 0.981

Gnomad NFE AF: 0.948

Gnomad OTH AF: 0.982

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

GnomAD4 genome AF: 0.969 AC: 147532 AN: 152220 Hom.: 71519 Cov.: 30 AF XY: 0.972 AC XY: 72334 AN XY: 74404

African (AFR) AF: 0.990 AC: 41144 AN: 41552

American (AMR) AF: 0.980 AC: 14976 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.985 AC: 3421 AN: 3472

East Asian (EAS) AF: 1.00 AC: 5152 AN: 5154

South Asian (SAS) AF: 0.992 AC: 4778 AN: 4818

European-Finnish (FIN) AF: 0.972 AC: 10298 AN: 10598

Middle Eastern (MID) AF: 0.980 AC: 288 AN: 294

European-Non Finnish (NFE) AF: 0.948 AC: 64500 AN: 68030

Other (OTH) AF: 0.982 AC: 2073 AN: 2110

Alfa AF: 0.957 Hom.: 166271

Bravo AF: 0.970

Asia WGS AF: 0.995 AC: 3458 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.17
DANN	Benign	0.57
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs6431731; hg19: chr2-15863002;