Genetic Variant ENSG00000254951:n.353+10438G>A (chr11-7895165-C-T) – ACMG Classification: Uncertain_significance (2 pts)

Variant summary

Our verdict is The variant received 2 classification points (ACGS-UK Somatic Oncogenicity v2025). O3_Moderate

The NR_036678.1(LOC283299):n.353+10438G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. Note: NR_036678.1 is not a MANE Select or MANE Plus Clinical transcript for LOC283299; 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 0.00000658 (AC=1) in the gnomAD database across 151,976 control chromosomes (no homozygotes observed). The grpmax filtering allele frequency (95% CI) is 0.00000658. 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 0.0000066 ( 0 hom., cov: 32)

Consequence

LOC283299
NR_036678.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.410

Publications

2 publications found

Variant links:

Genes affected

ENSG00000254951 (HGNC:):

ENSG00000254951 links:

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new If you want to explore the variant's impact on the transcript NR_036678.1, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

Classification according to ACGS-UK Somatic Oncogenicity v2025

Classification was made for transcript:

Our verdict: Uncertain_significance. The variant received 2 points.

Show applied only (1)

Apply	Criterion Code & Title / Strength	Strength	Rationale / Clinical Context
	O3Absent or very rare in population		Absent or extremely rare in gnomAD (AC ≤ 2) — O3 moderate; GnomAD: AF = 0.000007, AC = 1 — absent/extremely rare (O3 moderate [+2])

Variant Effect in Transcripts

Automated classification analysis was done for transcript: NR_036678.1. You can select a different transcript below to see updated classification assignments.

RefSeq Transcripts

Sel.	Gene / Transcript	Tags	HGVSc / HGVSp	Effect	Exon rank	Protein / UniProt
	LOC283299 NR_036678.1		n.353+10438G>A	intron	Intron 1 of 7	Prot:

LOC283299 NR_036678.1

HGVSc / HGVSpn.353+10438G>A

Exon rankIntron 1 of 7

intron

Prot:

Ensembl Transcripts

Sel.	Gene / Transcript	Tags	HGVSc / HGVSp	Effect	Exon rank	Protein / UniProt
	ENSG00000254951 ENST00000527847.5	TSL:2	n.353+10438G>A	intron	Intron 1 of 7	Prot:
	ENSG00000254951 ENST00000718815.1		n.373+10438G>A	intron	Intron 2 of 2	Prot:

ENSG00000254951 ENST00000527847.5

TSL:2

HGVSc / HGVSpn.353+10438G>A

Exon rankIntron 1 of 7

intron

Prot:

ENSG00000254951 ENST00000718815.1

HGVSc / HGVSpn.373+10438G>A

Exon rankIntron 2 of 2

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 3 sources Large-scale international reference populations
GnomAD3 genomes	AF: 0.00000658	AC:1	Hom:0	AN:151976	Cov:32
GnomAD4 genome	AF: 0.00000658	AC:1	Hom:0	AN:151976	Cov:32
ALFA (dbGaP/dbSNP Allele Frequency Aggregator)	AF: 0.00	AC:0	Hom:2536	AN:114042	Cov:

Showing 3 sources

ClinVar

Not reported in ClinVar

Computational Scores

Algorithm	Calibrated pred.	Score
AlphaGenome AVI	Uncertain	12
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.6
DANN	Benign	0.73
GPN-Star LLR	N/A	0.18
GPN-Star score	N/A	-0.18
PhyloP100	Benign	-0.41

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.

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

Classification according to ACGS-UK Somatic Oncogenicity v2025

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

ClinVar

Computational Scores

Splicing Scores

MaveDB functional evidence ?

Publications

Other links and lift over

MaveDB functional evidence