rs4006531

Variant names:

• chr8-125855261-G-A
• rs4006531
• ENST00000651999.1:n.353-31577G>A

Your query was ambiguous. Multiple possible variants found:

• chr8-125855261-G-A
• chr8-125855261-G-C
• chr8-125855261-G-T

Variant summary

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

The ENST00000651999.1(LINC02964):​n.353-31577G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.578 in 152,026 control chromosomes in the GnomAD database, including 27,379 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 0.58 (27379 hom., cov: 33)
• Consequence: LINC02964 ENST00000651999.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.581
• Publications: 4 publications found

Genes affected

LINC02964 (HGNC:53487): (long intergenic non-protein coding RNA 2964)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.678 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
LINC02964	ENST00000651999.1	n.353-31577G>A		intron_variant	Intron 5 of 7

Frequencies

GnomAD3 genomes AF: 0.579 AC: 87899 AN: 151908 Hom.: 27360 Cov.: 33

Gnomad AFR AF: 0.350

Gnomad AMI AF: 0.741

Gnomad AMR AF: 0.685

Gnomad ASJ AF: 0.558

Gnomad EAS AF: 0.379

Gnomad SAS AF: 0.559

Gnomad FIN AF: 0.751

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.683

Gnomad OTH AF: 0.566

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

GnomAD4 genome AF: 0.578 AC: 87944 AN: 152026 Hom.: 27379 Cov.: 33 AF XY: 0.582 AC XY: 43273 AN XY: 74328

African (AFR) AF: 0.350 AC: 14496 AN: 41420

American (AMR) AF: 0.685 AC: 10473 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.558 AC: 1937 AN: 3472

East Asian (EAS) AF: 0.379 AC: 1958 AN: 5160

South Asian (SAS) AF: 0.561 AC: 2706 AN: 4826

European-Finnish (FIN) AF: 0.751 AC: 7935 AN: 10564

Middle Eastern (MID) AF: 0.517 AC: 151 AN: 292

European-Non Finnish (NFE) AF: 0.683 AC: 46433 AN: 67988

Other (OTH) AF: 0.559 AC: 1179 AN: 2108

Alfa AF: 0.645 Hom.: 59392

Bravo AF: 0.563

Asia WGS AF: 0.421 AC: 1463 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.64
DANN	Benign	0.72
PhyloP100		-0.58

Splicing

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

Other links and lift over

dbSNP: rs4006531; hg19: chr8-126867505;