Genetic Variant ENSG00000297913:n.108-16681A>T (chr1-159709846-A-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 ENST00000751816.1(ENSG00000297913):n.108-16681A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. Note: ENST00000751816.1 is not a MANE Select or MANE Plus Clinical transcript for ENSG00000297913; 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 0.0000131 (AC=2) in the gnomAD database across 152,146 control chromosomes (no homozygotes observed). The grpmax filtering allele frequency (95% CI) is 0.0000654. 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 0.000013 ( 0 hom., cov: 32)

Consequence

ENSG00000297913
ENST00000751816.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.790

Publications

93 publications found

Variant links:

Genes affected

ENSG00000297913 (HGNC:):

ENSG00000297913 links:

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new If you want to explore the variant's impact on the transcript ENST00000751816.1, 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 = 0.000065, AC = 2 — absent/extremely rare (O3 moderate [+2])

Variant Effect in Transcripts

Automated classification analysis was done for transcript: ENST00000751816.1. You can select a different transcript below to see updated classification assignments.

RefSeq Transcripts

There are no transcript annotations for this variant.

Ensembl Transcripts

Gene / Transcript	HGVSc / HGVSp	Effect	Exon rank	Protein / UniProt
ENSG00000297913 ENST00000751816.1	n.108-16681A>T	intron	Intron 1 of 2	Prot:
ENSG00000297913 ENST00000751817.1	n.110-16681A>T	intron	Intron 1 of 3	Prot:
ENSG00000297913 ENST00000751818.1	n.63-16681A>T	intron	Intron 1 of 2	Prot:

ENSG00000297913 ENST00000751816.1

HGVSc / HGVSpn.108-16681A>T

Exon rankIntron 1 of 2

intron

Prot:

ENSG00000297913 ENST00000751817.1

HGVSc / HGVSpn.110-16681A>T

Exon rankIntron 1 of 3

intron

Prot:

ENSG00000297913 ENST00000751818.1

HGVSc / HGVSpn.63-16681A>T

Exon rankIntron 1 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 4 sources Large-scale international reference populations
GnomAD3 genomes	AF: 0.0000131	AC:2	Hom:0	AN:152146	Cov:32
GnomAD4 genome	AF: 0.0000131	AC:2	Hom:0	AN:152146	Cov:32
TOPMed (Bravo) Warning	AF: 0.0000264	AC:7	Hom:0	AN:264690	Cov:
ALFA (dbGaP/dbSNP Allele Frequency Aggregator)	AF: 0.00	AC:0	Hom:3343	AN:525352	Cov:
Local & regional cohorts 1 source Population-specific and national genomic databases
ABraOM SABE-WGS-1171	AF: 0.000548	AC:1	Hom:0	AN:1824	Cov:

Showing 5 sources

Tested, but no data found:GnomAD4 exomeIf GnomAD4 is missing, the position is probably not covered by the project.

ClinVar

Not reported in ClinVar

Computational Scores

Algorithm	Calibrated pred.	Score
AlphaGenome AVI	Benign	1.3
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.52
DANN	Benign	0.69
GPN-Star LLR	N/A	0.28
GPN-Star score	N/A	-0.28
PhyloP100	Benign	-0.79

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