rs10771657

Variant names:

• chr12-30206361-C-T
• rs10771657
• ENST00000549055.1:n.127-2081C>T

Variant summary

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

The ENST00000549055.1(ENSG00000257262):​n.127-2081C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.378 in 152,090 control chromosomes in the GnomAD database, including 11,629 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 0.38 (11629 hom., cov: 32)
• Consequence: ENSG00000257262 ENST00000549055.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.346
• Publications: 4 publications found

Genes affected

ENSG00000257262 (HGNC:):

LINC02386 (HGNC:53312): (long intergenic non-protein coding RNA 2386)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.495 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000257262	ENST00000549055.1	n.127-2081C>T		intron_variant	Intron 1 of 2	3
LINC02386	ENST00000824524.1	n.170-6722G>A		intron_variant	Intron 2 of 2
LINC02386	ENST00000824525.1	n.224-6722G>A		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.378 AC: 57443 AN: 151972 Hom.: 11616 Cov.: 32

Gnomad AFR AF: 0.228

Gnomad AMI AF: 0.412

Gnomad AMR AF: 0.496

Gnomad ASJ AF: 0.464

Gnomad EAS AF: 0.511

Gnomad SAS AF: 0.394

Gnomad FIN AF: 0.382

Gnomad MID AF: 0.434

Gnomad NFE AF: 0.425

Gnomad OTH AF: 0.391

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

GnomAD4 genome AF: 0.378 AC: 57472 AN: 152090 Hom.: 11629 Cov.: 32 AF XY: 0.379 AC XY: 28154 AN XY: 74336

African (AFR) AF: 0.228 AC: 9453 AN: 41486

American (AMR) AF: 0.497 AC: 7591 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.464 AC: 1608 AN: 3466

East Asian (EAS) AF: 0.511 AC: 2638 AN: 5158

South Asian (SAS) AF: 0.395 AC: 1904 AN: 4820

European-Finnish (FIN) AF: 0.382 AC: 4038 AN: 10568

Middle Eastern (MID) AF: 0.425 AC: 125 AN: 294

European-Non Finnish (NFE) AF: 0.425 AC: 28915 AN: 67994

Other (OTH) AF: 0.390 AC: 824 AN: 2112

Alfa AF: 0.411 Hom.: 17066

Bravo AF: 0.380

Asia WGS AF: 0.444 AC: 1546 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.83
DANN	Benign	0.53
PhyloP100		-0.35

Splicing

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

Other links and lift over

dbSNP: rs10771657; hg19: chr12-30359294;