rs10125054

Variant names:

• chr9-112035757-G-A
• rs10125054
• ENST00000563434.1:n.1286C>T

Your query was ambiguous. Multiple possible variants found:

• chr9-112035757-G-A
• chr9-112035757-G-C

Variant summary

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

The ENST00000563434.1(LINC02977):​n.1286C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.268 in 152,142 control chromosomes in the GnomAD database, including 5,575 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 0.27 (5575 hom., cov: 32)
  • Exomes 𝑓: 0.33 (0 hom.)
• Consequence: LINC02977 ENST00000563434.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.793
• Publications: 13 publications found

Genes affected

LINC02977 (HGNC:56036): (long intergenic non-protein coding RNA 2977)

ENSG00000299696 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.382 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000563434.1. 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
	LINC02977	NR_186812.1		n.2246+2422C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02977	ENST00000563434.1	TSL:2	n.1286C>T		non_coding_transcript_exon	Exon 2 of 2
	LINC02977	ENST00000568421.1	TSL:6	n.554C>T		non_coding_transcript_exon	Exon 1 of 1
	LINC02977	ENST00000658557.1		n.965+2422C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.268 AC: 40789 AN: 152020 Hom.: 5579 Cov.: 32

Gnomad AFR AF: 0.285

Gnomad AMI AF: 0.182

Gnomad AMR AF: 0.263

Gnomad ASJ AF: 0.294

Gnomad EAS AF: 0.397

Gnomad SAS AF: 0.314

Gnomad FIN AF: 0.310

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.239

Gnomad OTH AF: 0.278

GnomAD4 exome AF: 0.333 AC: 2 AN: 6 Hom.: 0 Cov.: 0 AF XY: 0.333 AC XY: 2 AN XY: 6

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.500 AC: 1 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.250 AC: 1 AN: 4

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.268 AC: 40806 AN: 152136 Hom.: 5575 Cov.: 32 AF XY: 0.273 AC XY: 20338 AN XY: 74376

African (AFR) AF: 0.285 AC: 11819 AN: 41474

American (AMR) AF: 0.263 AC: 4025 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.294 AC: 1019 AN: 3466

East Asian (EAS) AF: 0.396 AC: 2055 AN: 5184

South Asian (SAS) AF: 0.314 AC: 1513 AN: 4818

European-Finnish (FIN) AF: 0.310 AC: 3277 AN: 10576

Middle Eastern (MID) AF: 0.269 AC: 79 AN: 294

European-Non Finnish (NFE) AF: 0.239 AC: 16271 AN: 68012

Other (OTH) AF: 0.276 AC: 582 AN: 2112

Alfa AF: 0.248 Hom.: 12909

Bravo AF: 0.266

Asia WGS AF: 0.330 AC: 1145 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	7.2
DANN	Benign	0.73
PhyloP100		0.79

Splicing

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

Other links and lift over

dbSNP: rs10125054; hg19: chr9-114798037; COSMIC: COSV73721038;