rs2327484

Variant names:

• chr6-134412590-A-C
• rs2327484
• ENST00000431422.3:n.54-24725A>C

Your query was ambiguous. Multiple possible variants found:

• chr6-134412590-A-C
• chr6-134412590-A-G

Variant summary

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

The ENST00000431422.3(LINC01010):​n.54-24725A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.325 in 152,148 control chromosomes in the GnomAD database, including 12,912 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 0.32 (12912 hom., cov: 32)
• Consequence: LINC01010 ENST00000431422.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.01
• Publications: 1 publications found

Genes affected

LINC01010 (HGNC:48978): (long intergenic non-protein coding RNA 1010)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.717 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000431422.3. 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
	LINC01010	ENST00000431422.3	TSL:2	n.54-24725A>C		intron	N/A
	LINC01010	ENST00000660399.1		n.54-52151A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.325 AC: 49343 AN: 152030 Hom.: 12881 Cov.: 32

Gnomad AFR AF: 0.723

Gnomad AMI AF: 0.333

Gnomad AMR AF: 0.218

Gnomad ASJ AF: 0.341

Gnomad EAS AF: 0.158

Gnomad SAS AF: 0.175

Gnomad FIN AF: 0.102

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.162

Gnomad OTH AF: 0.335

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

GnomAD4 genome AF: 0.325 AC: 49413 AN: 152148 Hom.: 12912 Cov.: 32 AF XY: 0.316 AC XY: 23518 AN XY: 74402

African (AFR) AF: 0.723 AC: 29986 AN: 41452

American (AMR) AF: 0.218 AC: 3332 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.341 AC: 1183 AN: 3472

East Asian (EAS) AF: 0.158 AC: 818 AN: 5174

South Asian (SAS) AF: 0.174 AC: 839 AN: 4818

European-Finnish (FIN) AF: 0.102 AC: 1081 AN: 10608

Middle Eastern (MID) AF: 0.405 AC: 119 AN: 294

European-Non Finnish (NFE) AF: 0.163 AC: 11053 AN: 68014

Other (OTH) AF: 0.331 AC: 699 AN: 2112

Alfa AF: 0.245 Hom.: 5745

Bravo AF: 0.352

Asia WGS AF: 0.190 AC: 661 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	0.42
DANN	Benign	0.31
PhyloP100		-2.0

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: rs2327484;

hg19: chr6-134733728;