15-78559273-G-A

Variant names:

• chr15-78559273-G-A
• rs2036527

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 15-78559273-G-A has been identified. The variant allele was found at a cumulative frequency of 0.288 (AC=43,744) in the gnomAD database across 152,096 control chromosomes, including 6,845 homozygotes. The grpmax filtering allele frequency (95% CI) is 0.346. 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 0.29 (6845 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.762
• Publications: 127 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 = 0.3461 — 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: 0.288	AC:43709	Hom:6838	AN:151978	Cov:33
GnomAD4 genome	AF: 0.288	AC:43744	Hom:6845	AN:152096	Cov:33
TOPMed (Bravo)	AF: 0.277	AC:	Hom:	AN:	Cov:
ALFA (dbGaP/dbSNP Allele Frequency Aggregator)	AF: 0.322	AC:204883	Hom:34359	AN:636018	Cov:
Local & regional cohorts 10 sources Population-specific and national genomic databases
ABraOM SABE-WGS-1171	AF: 0.305	AC:715	Hom:126	AN:2342	Cov:
ChinaMAP Phase 1	AF: 0.0312	AC:	Hom:	AN:	Cov:
Denmark Genome	AF: 0.410	AC:123	Hom:	AN:300	Cov:
GenomeAsia100K	AF: 0.134	AC:470	Hom:	AN:3478	Cov:
Korea4K (4,157 Koreans)	AF: 0.0240	AC:177	Hom:	AN:7232	Cov:
Qatari Genome	AF: 0.375	AC:66	Hom:	AN:176	Cov:
ToMMo 61KJPN (+60KJPN MNV)	AF: 0.0228	AC:2800	Hom:33	AN:122680	Cov:
Turkish Variome	AF: 0.367	AC:568	Hom:111	AN:1546	Cov:
UK10K	AF: 0.328	AC:2477	Hom:	AN:7562	Cov:
WBBC (Westlake BioBank for Chinese) pilot	AF: 0.0301	AC:270	Hom:6	AN:8960	Cov:

Showing 14 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	Prediction
AlphaGenome AVI	Uncertain	11
BayesDel_noAF	Benign	-0.79
CADD	Benign	11
DANN	Benign	0.47
GPN-Star LLR	N/A	-2.7
GPN-Star score	N/A	2.7
PhyloP100	Benign	0.76

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: rs2036527;

hg19: chr15-78851615;

ACMG debug oncogenicity

ACGS debug oncogenicity

ACMG debug germline

Submit to ClinVar