rs1978238

chr12-3322405-C-Achr12-3322405-C-Gchr12-3322405-C-T

Variant summary

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

The NR_148995.1(LOC100128253):n.65-14587G>T 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 0.577 in 151,944 control chromosomes in the GnomAD database, including 25,716 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 (25716 hom., cov: 32)
• Consequence: LOC100128253 NR_148995.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.258

Genes affected

LINC02827 (HGNC:54358): (long intergenic non-protein coding RNA 2827)

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.631 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC100128253	NR_148995.1	n.65-14587G>T		intron_variant, non_coding_transcript_variant
LINC02827	XR_007063165.1	n.2742-944C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02827	ENST00000432994.2	n.1010-944C>A		intron_variant, non_coding_transcript_variant		2
	ENST00000635814.1	n.273+919G>T		intron_variant, non_coding_transcript_variant
	ENST00000636557.1	n.65-14587G>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.577 AC: 87621 AN: 151824 Hom.: 25698 Cov.: 32

Gnomad AFR AF: 0.497

Gnomad AMI AF: 0.573

Gnomad AMR AF: 0.600

Gnomad ASJ AF: 0.552

Gnomad EAS AF: 0.329

Gnomad SAS AF: 0.650

Gnomad FIN AF: 0.589

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.635

Gnomad OTH AF: 0.552

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

GnomAD4 genome AF: 0.577 AC: 87691 AN: 151944 Hom.: 25716 Cov.: 32 AF XY: 0.575 AC XY: 42734 AN XY: 74262

Gnomad4 AFR AF: 0.497

Gnomad4 AMR AF: 0.601

Gnomad4 ASJ AF: 0.552

Gnomad4 EAS AF: 0.330

Gnomad4 SAS AF: 0.650

Gnomad4 FIN AF: 0.589

Gnomad4 NFE AF: 0.635

Gnomad4 OTH AF: 0.550

Alfa AF: 0.616 Hom.: 57452

Bravo AF: 0.572

Asia WGS AF: 0.513 AC: 1782 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	3.8
Dann	Benign	0.28

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1978238; hg19: chr12-3431571;