chr10-120670257-T-C

Variant names:

• chr10-120670257-T-C
• rs7475474
• ENST00000655330.1:n.340+34108T>C

GermlineCancer (beta)

Variant summary

Our verdict is Benign.

<-10 Benign

-7

-6

-1

0

+5

+6

+9

+10

BenignB

Likely BenignLB

UncertainVUS

Likely PathogenicLP

PathogenicP

The variant received -12 classification points (ACMG Germline Pathogenicity v2019). BA1BP4_Strong

The XR_002957103.2(LINC02930):n.400+34108T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. Note: XR_002957103.2 is not a MANE Select or MANE Plus Clinical transcript for LINC02930; the reported annotation may differ from that of the MANE-designated reference transcript for this gene. The variant allele was found at a cumulative frequency of 0.388 (AC=58,956) in the gnomAD database across 151,902 control chromosomes, including 11,658 homozygotes. The grpmax filtering allele frequency (95% CI) is 0.475. In-silico predictor (BayesDel (noAF)) classifies this variant as likely benign. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.39 (11658 hom., cov: 31)
• Consequence: LINC02930 XR_002957103.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.875
• Publications: 3 publications found

Genes affected

LINC02930 (HGNC:55821): ()

Classification according to ACMG Germline Pathogenicity v2019

Classification was made for transcript:

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

Apply	Criterion Code & Title / Strength	Strength	Rationale / Clinical Context
	BP4Computational evidence suggests no impact		Computational evidence supports benign — no pathogenic computational or splicing signal (BP4); No splicing predictor data available.; Germline computational verdict: benign (Strong).
	BA1Stand-alone benign allele frequency (>5%)		GnomAD effective popmax AF >5% — BA1 stand-alone benign; GnomAD reliable popmax AF = 0.4747 — exceeds 5%% threshold (BA1 applied)

Variant Effect in Transcripts

Automated classification analysis was done for transcript: ENST00000655330.1. You can select a different transcript below to see updated classification assignments.

RefSeq Transcripts

There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene / Transcript	Tags	HGVSc / HGVSp	Effect	Exon rank	Protein / UniProt
	LINC02930 ENST00000655330.1		n.340+34108T>C	intron	Intron 2 of 3	Prot:
	LINC02930 ENST00000659883.1		n.402+34108T>C	intron	Intron 2 of 6	Prot:
	LINC02930 ENST00000663713.2		n.402+34108T>C	intron	Intron 2 of 4	Prot:

LINC02930 ENST00000655330.1

HGVSc / HGVSpn.340+34108T>C

Exon rankIntron 2 of 3

intron

Prot:

LINC02930 ENST00000659883.1

HGVSc / HGVSpn.402+34108T>C

Exon rankIntron 2 of 6

intron

Prot:

LINC02930 ENST00000663713.2

HGVSc / HGVSpn.402+34108T>C

Exon rankIntron 2 of 4

intron

Prot:

Frequencies

Allele frequencies (AF), counts (AC/AN), homozygotes and coverage

Common (AF > 0.05 / Hom > 5)

Rare (AF ≤ 0.0001 / Hom ≤ 1)

Source / population	AF	AC	Hom	AN	Coverage
Global population databases 4 sources Large-scale international reference populations
GnomAD3 genomes	AF: 0.388	AC:58927	Hom:11654	AN:151784	Cov:31
GnomAD4 genome	AF: 0.388	AC:58956	Hom:11658	AN:151902	Cov:31
TOPMed (Bravo)	AF: 0.391	AC:103568	Hom:20768	AN:264690	Cov:
ALFA (dbGaP/dbSNP Allele Frequency Aggregator)	AF: 0.400	AC:30869	Hom:6259	AN:77094	Cov:
Local & regional cohorts 10 sources Population-specific and national genomic databases
ABraOM SABE-WGS-1171	AF: 0.423	AC:990	Hom:200	AN:2342	Cov:
ChinaMAP Phase 1	AF: 0.505	AC:	Hom:	AN:	Cov:
Denmark Genome	AF: 0.360	AC:108	Hom:	AN:300	Cov:
GenomeAsia100K	AF: 0.447	AC:1555	Hom:	AN:3478	Cov:
Korea4K (4,157 Koreans)	AF: 0.563	AC:4068	Hom:	AN:7232	Cov:
Qatari Genome	AF: 0.295	AC:52	Hom:	AN:176	Cov:
ToMMo 61KJPN (+60KJPN MNV)	AF: 0.591	AC:72554	Hom:21499	AN:122800	Cov:
Turkish Variome	AF: 0.382	AC:591	Hom:133	AN:1546	Cov:
UK10K	AF: 0.402	AC:3040	Hom:	AN:7562	Cov:
WBBC (Westlake BioBank for Chinese) pilot	AF: 0.497	AC:4451	Hom:1142	AN:8960	Cov:

Showing 14 sources

ClinVar

Not reported in ClinVar

Computational Scores

Algorithm	Calibrated pred.	Score	Prediction
AlphaGenome AVI	Benign	1.3
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.59
DANN	Benign	0.36
GPN-Star LLR	N/A	4.2
GPN-Star score	N/A	-0.53
PhyloP100	Benign	-0.88

Showing 7 of 7 scores

Splicing Scores

No splicing scores have been computed for this variant.

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

MaveDB functional evidence

MaveDB is a public repository of laboratory assays that test the effect of thousands of variants at once — treat this as supporting research data and interpret it with great caution; it is not a clinical classification.

No MaveDB functional evidence found for this variant.

Other links and lift over

dbSNP: rs7475474;

hg19: chr10-122429769;

ACMG debug oncogenicity

ACGS debug oncogenicity

ACMG debug germline

Submit to ClinVar