chr17-30315362-T-C

Variant names:

• chr17-30315362-T-C
• rs8081598

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 variant 17-30315362-T-C has been identified. The variant allele was found at a cumulative frequency of 0.104 (AC=15,806) in the gnomAD database across 152,276 control chromosomes, including 1,496 homozygotes. The grpmax filtering allele frequency (95% CI) is 0.244. 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 0.10 (1496 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.128
• Publications: 0 publications found

Classification according to ACMG Germline Pathogenicity v2019

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 = 0.2441 — exceeds 5%% threshold (BA1 applied)

Variant Effect in Transcripts

 

RefSeq Transcripts

There are no transcript annotations for this variant.

Ensembl Transcripts

There are no transcript annotations for this variant.

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: 0.104	AC:15785	Hom:1493	AN:152158	Cov:32
GnomAD4 genome	AF: 0.104	AC:15806	Hom:1496	AN:152276	Cov:32
TOPMed (Bravo)	AF: 0.110	AC:	Hom:	AN:	Cov:
ALFA (dbGaP/dbSNP Allele Frequency Aggregator)	AF: 0.0719	AC:15106	Hom:984	AN:210068	Cov:
Local & regional cohorts 10 sources Population-specific and national genomic databases
ABraOM SABE-WGS-1171	AF: 0.0914	AC:214	Hom:11	AN:2342	Cov:
ChinaMAP Phase 1	AF: 0.0604	AC:	Hom:	AN:	Cov:
Denmark Genome	AF: 0.0100	AC:3	Hom:	AN:300	Cov:
GenomeAsia100K	AF: 0.0800	AC:279	Hom:	AN:3478	Cov:
Korea4K (4,157 Koreans)	AF: 0.0290	AC:212	Hom:	AN:7234	Cov:
Qatari Genome	AF: 0.114	AC:20	Hom:	AN:176	Cov:
ToMMo 61KJPN (+60KJPN MNV)	AF: 0.0104	AC:1277	Hom:10	AN:122768	Cov:
Turkish Variome	AF: 0.0602	AC:93	Hom:4	AN:1546	Cov:
UK10K	AF: 0.0409	AC:309	Hom:	AN:7562	Cov:
WBBC (Westlake BioBank for Chinese) pilot	AF: 0.0577	AC:517	Hom:23	AN:8960	Cov:

Showing 14 sources

ClinVar

Not reported in ClinVar

Computational Scores

Algorithm	Calibrated pred.	Score	Prediction
AlphaGenome AVI	Benign	1.6
BayesDel_noAF	Benign	-0.57
CADD	Benign	12
DANN	Benign	0.90
GPN-Star LLR	N/A	-1.5
GPN-Star score	N/A	1.5
PhyloP100	Benign	-0.13

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: rs8081598;

hg19: chr17-28642380;

ACMG debug oncogenicity

ACGS debug oncogenicity

ACMG debug germline

Submit to ClinVar