rs1431918

Positions:

• chr8-61973294-G-A
• chr8-61973294-G-T

Variant summary

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

The XR_428354.4(LINC02842):​n.1060+794G>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 0.326 in 151,890 control chromosomes in the GnomAD database, including 9,224 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 0.33 (9224 hom., cov: 32)
• Consequence: LINC02842 XR_428354.4 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.91

Genes affected

LINC02842 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.486 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02842	XR_001745926.3	n.1060+794G>A		intron_variant, non_coding_transcript_variant
LINC02842	XR_007060925.1	n.1017+794G>A		intron_variant, non_coding_transcript_variant
LINC02842	XR_007060931.1	n.1017+794G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.326 AC: 49467 AN: 151772 Hom.: 9220 Cov.: 32

Gnomad AFR AF: 0.151

Gnomad AMI AF: 0.255

Gnomad AMR AF: 0.297

Gnomad ASJ AF: 0.330

Gnomad EAS AF: 0.321

Gnomad SAS AF: 0.502

Gnomad FIN AF: 0.378

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.419

Gnomad OTH AF: 0.323

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

GnomAD4 genome AF: 0.326 AC: 49480 AN: 151890 Hom.: 9224 Cov.: 32 AF XY: 0.326 AC XY: 24207 AN XY: 74202

Gnomad4 AFR AF: 0.151

Gnomad4 AMR AF: 0.297

Gnomad4 ASJ AF: 0.330

Gnomad4 EAS AF: 0.321

Gnomad4 SAS AF: 0.503

Gnomad4 FIN AF: 0.378

Gnomad4 NFE AF: 0.419

Gnomad4 OTH AF: 0.330

Alfa AF: 0.403 Hom.: 7344

Bravo AF: 0.312

Asia WGS AF: 0.423 AC: 1473 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.017
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1431918; hg19: chr8-62885853; COSMIC: COSV69466666;