rs326882

Variant names:

• chr4-111806971-G-A
• rs326882
• ENST00000506068.1:n.83+4088G>A

Your query was ambiguous. Multiple possible variants found:

• chr4-111806971-G-A
• chr4-111806971-G-C

Variant summary

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

The ENST00000506068.1(ENSG00000250855):​n.83+4088G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.505 in 151,770 control chromosomes in the GnomAD database, including 21,680 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 0.50 (21680 hom., cov: 31)
• Consequence: ENSG00000250855 ENST00000506068.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.14
• Publications: 1 publications found

Genes affected

ENSG00000250855 (HGNC:):

LINC02945 (HGNC:55960): (long intergenic non-protein coding RNA 2945)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.628 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000506068.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02945	NR_186683.1		n.209-2378C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000250855	ENST00000506068.1	TSL:3	n.83+4088G>A		intron	N/A
	LINC02945	ENST00000508010.2	TSL:5	n.475-2378C>T		intron	N/A
	LINC02945	ENST00000797993.1		n.444+1426C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.505 AC: 76597 AN: 151652 Hom.: 21673 Cov.: 31

Gnomad AFR AF: 0.240

Gnomad AMI AF: 0.706

Gnomad AMR AF: 0.502

Gnomad ASJ AF: 0.624

Gnomad EAS AF: 0.423

Gnomad SAS AF: 0.517

Gnomad FIN AF: 0.698

Gnomad MID AF: 0.440

Gnomad NFE AF: 0.633

Gnomad OTH AF: 0.536

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

GnomAD4 genome AF: 0.505 AC: 76604 AN: 151770 Hom.: 21680 Cov.: 31 AF XY: 0.507 AC XY: 37628 AN XY: 74190

African (AFR) AF: 0.240 AC: 9892 AN: 41302

American (AMR) AF: 0.501 AC: 7645 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.624 AC: 2165 AN: 3470

East Asian (EAS) AF: 0.422 AC: 2179 AN: 5158

South Asian (SAS) AF: 0.517 AC: 2488 AN: 4808

European-Finnish (FIN) AF: 0.698 AC: 7366 AN: 10556

Middle Eastern (MID) AF: 0.432 AC: 127 AN: 294

European-Non Finnish (NFE) AF: 0.633 AC: 42962 AN: 67910

Other (OTH) AF: 0.539 AC: 1136 AN: 2106

Alfa AF: 0.540 Hom.: 8313

Bravo AF: 0.476

Asia WGS AF: 0.501 AC: 1747 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.51
DANN	Benign	0.64
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs326882; hg19: chr4-112728127;