rs326882

Positions:

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

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000506068.1(ENSG00000250855):​n.83+4088G>A variant causes a intron, non coding transcript 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: ENST00000506068.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.14

Genes affected

(HGNC:):

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000506068.1	n.83+4088G>A		intron_variant, non_coding_transcript_variant		3
LINC02945	ENST00000508010.1	n.125-2378C>T		intron_variant, non_coding_transcript_variant		5

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

Gnomad4 AFR AF: 0.240

Gnomad4 AMR AF: 0.501

Gnomad4 ASJ AF: 0.624

Gnomad4 EAS AF: 0.422

Gnomad4 SAS AF: 0.517

Gnomad4 FIN AF: 0.698

Gnomad4 NFE AF: 0.633

Gnomad4 OTH AF: 0.539

Alfa AF: 0.541 Hom.: 4337

Bravo AF: 0.476

Asia WGS AF: 0.501 AC: 1747 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs326882; hg19: chr4-112728127;